mock_pbrun.py

import argparse
import json
import random
import time
from pathlib import Path
from urllib.parse import quote
from urllib.request import urlopen

PATHOGENIC_VARIANTS = [
    ("chr2", 179441812, "G", "A", "TTN-AS1", 93.8, "LowQual"),
    ("chr2", 179442065, "G", "T", "TTN-AS1", 89.6, "PASS"),
    ("chr2", 233350807, "G", "C", "ECEL1", 73.7, "LowQual"),
    ("chr2", 234235799, "C", "T", "SAG", 98.9, "PASS"),
    ("chr2", 234237155, "C", "T", "SAG", 71.4, "LowQual"),
    ("chr2", 234237260, "G", "C", "SAG", 68.3, "PASS"),
    ("chr2", 234243644, "G", "A", "SAG", 70.6, "PASS"),
    ("chr17", 41244307, "T", "C", "BRCA1", 78.2, "PASS"),
    ("chr2", 179406131, "C", "T", "TTN-AS1", 79.7, "PASS"),
    ("chr2", 31805960, "G", "A", "SRD5A2", 54.2, "LowQual"),
    ("chr2", 228564274, "T", "C", "SLC19A3", 58.5, "LowQual"),
    ("chr3", 11067523, "C", "T", "SLC6A1", 65.3, "LowQual"),
    ("chr3", 11067528, "G", "A", "SLC6A1", 86.2, "LowQual"),
    ("chr17", 41244538, "C", "A", "BRCA1", 76.8, "LowQual"),
    ("chr2", 32352025, "A", "G", "SPAST", 51.7, "PASS"),
    ("chr2", 47643454, "C", "G", "MSH2", 95.8, "PASS"),
    ("chr2", 179418346, "C", "T", "TTN-AS1", 68.2, "PASS"),
    ("chr2", 179396702, "C", "T", "TTN-AS1", 91.6, "LowQual"),
    ("chr2", 32353535, "T", "G", "SPAST", 87.1, "LowQual"),
    ("chr2", 32353552, "A", "G", "SPAST", 52.5, "LowQual"),
    ("chr2", 32361638, "G", "A", "SPAST", 70.5, "LowQual"),
    ("chr3", 122002743, "C", "T", "CASR", 91.1, "PASS"),
    ("chr2", 207636997, "C", "G", "FASTKD2", 95.2, "PASS"),
    ("chr2", 233399923, "A", "G", "CHRND", 54.8, "PASS"),
    ("chr2", 179424524, "G", "A", "TTN-AS1", 78.9, "PASS"),
    ("chr17", 41245498, "G", "A", "BRCA1", 50.7, "PASS"),
    ("chr2", 179426671, "C", "T", "TTN-AS1", 52.9, "PASS"),
    ("chr2", 48023174, "C", "G", "MSH6", 74.7, "PASS"),
    ("chr2", 47702251, "C", "G", "MSH2", 78.9, "PASS"),
    ("chr2", 38298092, "G", "A", "CYP1B1", 74.4, "LowQual"),
    ("chr2", 179430158, "T", "C", "TTN-AS1", 86.8, "LowQual"),
    ("chr2", 233633329, "G", "A", "GIGYF2", 91.0, "PASS"),
    ("chr2", 208993020, "G", "C", "CRYGC", 52.0, "PASS"),
    ("chr2", 211464106, "T", "G", "CPS1", 66.5, "PASS"),
    ("chr2", 47637509, "C", "T", "MSH2", 82.2, "LowQual"),
    ("chr2", 210640757, "C", "T", "UNC80", 70.2, "LowQual"),
    ("chr2", 47705646, "C", "T", "MSH2", 62.0, "PASS"),
    ("chr2", 210642081, "G", "C", "UNC80", 65.3, "PASS"),
    ("chr3", 123015063, "G", "T", "ADCY5", 64.7, "PASS"),
    ("chr2", 179398989, "C", "T", "TTN-AS1", 97.9, "PASS"),
    ("chr17", 41244902, "A", "T", "BRCA1", 60.7, "PASS"),
    ("chr2", 48010373, "A", "G", "MSH6", 75.6, "PASS"),
    ("chr2", 39281922, "T", "C", "SOS1", 64.1, "PASS"),
    ("chr2", 39283845, "T", "C", "SOS1", 87.2, "PASS"),
    ("chr17", 41245710, "C", "A", "BRCA1", 73.3, "PASS"),
    ("chr17", 41245846, "G", "A", "BRCA1", 62.6, "PASS"),
    ("chr17", 41245848, "T", "G", "BRCA1", 65.0, "PASS"),
]

OTHER_VARIANTS = [
    ("chr2", 179441492, "C", "T", "TTN-AS1", 61.0, "PASS"),
    ("chr2", 191934481, "G", "A", "STAT4", 50.7, "PASS"),
    ("chr2", 179441541, "C", "T", "TTN-AS1", 83.1, "PASS"),
    ("chr2", 191937866, "C", "T", "STAT4", 79.8, "PASS"),
    ("chr2", 191937890, "A", "G", "STAT4", 86.1, "PASS"),
    ("chr2", 179441811, "C", "T", "TTN-AS1", 92.0, "PASS"),
    ("chr2", 179441842, "A", "T", "TTN-AS1", 53.5, "PASS"),
    ("chr2", 1920724, "C", "G", "MYT1L", 81.3, "PASS"),
    ("chr2", 179441903, "A", "G", "TTN-AS1", 83.9, "LowQual"),
    ("chr2", 1921052, "C", "T", "MYT1L", 88.8, "PASS"),
    ("chr2", 1921079, "A", "G", "MYT1L", 77.3, "PASS"),
    ("chr2", 179441966, "A", "G", "TTN-AS1", 67.8, "PASS"),
    ("chr2", 192255166, "A", "G", "MYO1B", 93.2, "PASS"),
    ("chr2", 179442126, "G", "T", "TTN-AS1", 57.1, "PASS"),
    ("chr2", 192267404, "A", "T", "MYO1B", 94.0, "PASS"),
    ("chr2", 179442176, "A", "G", "TTN-AS1", 89.6, "PASS"),
    ("chr2", 192279339, "A", "G", "MYO1B", 88.8, "PASS"),
    ("chr2", 179442324, "C", "G", "TTN-AS1", 71.0, "PASS"),
    ("chr2", 1926129, "C", "T", "MYT1L", 86.1, "PASS"),
    ("chr2", 1926194, "C", "T", "MYT1L", 72.3, "PASS"),
    ("chr2", 179442369, "T", "C", "TTN-AS1", 58.9, "PASS"),
    ("chr3", 119211211, "T", "C", "POGLUT1", 77.2, "PASS"),
    ("chr2", 233348908, "G", "A", "ECEL1", 80.8, "LowQual"),
    ("chr2", 233349181, "C", "A", "ECEL1", 74.2, "PASS"),
    ("chr2", 207169424, "C", "T", "ZDBF2", 56.9, "PASS"),
    ("chr2", 233350775, "C", "T", "ECEL1", 67.5, "LowQual"),
    ("chr3", 121981248, "G", "T", "CASR", 57.3, "PASS"),
    ("chr2", 37014404, "G", "A", "VIT", 85.7, "LowQual"),
    ("chr3", 121981259, "G", "A", "CASR", 79.6, "LowQual"),
    ("chr2", 47690288, "A", "T", "MSH2", 67.4, "PASS"),
    ("chr3", 122123173, "C", "T", "FAM162A", 50.4, "PASS"),
    ("chr2", 47703666, "C", "A", "MSH2", 72.6, "PASS"),
    ("chr2", 47703671, "C", "T", "MSH2", 82.5, "PASS"),
    ("chr3", 122134275, "T", "C", "WDR5B", 52.0, "PASS"),
    ("chr2", 209116213, "G", "A", "IDH1", 74.0, "PASS"),
    ("chr2", 47703679, "G", "T", "MSH2", 71.8, "LowQual"),
    ("chr2", 234235773, "G", "A", "SAG", 92.8, "PASS"),
    ("chr2", 39210303, "C", "T", "SOS1", 80.3, "PASS"),
    ("chr2", 209130989, "A", "G", "PIKFYVE", 59.9, "PASS"),
    ("chr2", 39210747, "A", "T", "SOS1", 82.1, "PASS"),
    ("chr2", 209138458, "G", "A", "PIKFYVE", 73.2, "PASS"),
    ("chr2", 209150454, "C", "A", "PIKFYVE", 51.4, "PASS"),
    ("chr2", 209168896, "G", "A", "PIKFYVE", 69.1, "LowQual"),
    ("chr3", 105258866, "A", "G", "ALCAM", 59.8, "PASS"),
    ("chr2", 30143119, "C", "T", "ALK", 96.3, "LowQual"),
    ("chr3", 105377971, "T", "A", "CBLB", 81.6, "PASS"),
    ("chr2", 30143134, "G", "C", "ALK", 82.4, "LowQual"),
    ("chr3", 120389380, "C", "A", "HGD", 75.3, "PASS"),
    ("chr3", 120389398, "A", "G", "HGD", 96.7, "LowQual"),
    ("chr3", 105397304, "G", "A", "CBLB", 53.8, "PASS"),
    ("chr2", 30143148, "C", "A", "ALK", 98.9, "PASS"),
    ("chr2", 30143149, "A", "G", "ALK", 89.9, "PASS"),
    ("chr3", 120876432, "C", "G", "STXBP5L", 93.3, "PASS"),
    ("chr2", 30143151, "C", "T", "ALK", 87.0, "PASS"),
    ("chr2", 30143164, "C", "T", "ALK", 72.5, "PASS"),
    ("chr2", 30143171, "C", "T", "ALK", 65.3, "PASS"),
    ("chr2", 209189698, "C", "T", "PIKFYVE", 99.2, "PASS"),
    ("chr2", 47703696, "T", "C", "MSH2", 91.9, "PASS"),
    ("chr2", 209190084, "C", "T", "PIKFYVE", 81.2, "PASS"),
    ("chr2", 39211574, "G", "A", "SOS1", 78.6, "PASS"),
    ("chr2", 47703701, "C", "G", "MSH2", 65.2, "LowQual"),
    ("chr2", 234243322, "T", "C", "SAG", 63.0, "LowQual"),
    ("chr2", 209190489, "A", "G", "PIKFYVE", 85.8, "PASS"),
    ("chr2", 234243643, "C", "T", "SAG", 97.6, "PASS"),
    ("chr3", 122277271, "G", "A", "PARP9", 52.0, "LowQual"),
    ("chr2", 47703722, "T", "C", "MSH2", 78.2, "LowQual"),
    ("chr2", 39213001, "A", "G", "SOS1", 54.9, "PASS"),
    ("chr2", 209195396, "C", "G", "PIKFYVE", 82.4, "PASS"),
    ("chr3", 122287963, "C", "G", "DTX3L", 65.4, "LowQual"),
    ("chr3", 122288125, "T", "C", "DTX3L", 90.0, "PASS"),
    ("chr2", 209200043, "C", "T", "PIKFYVE", 84.1, "LowQual"),
    ("chr3", 121151250, "G", "C", "POLQ", 87.2, "PASS"),
    ("chr3", 121151879, "T", "A", "POLQ", 60.0, "PASS"),
    ("chr3", 121155074, "T", "C", "POLQ", 92.5, "PASS"),
    ("chr3", 121168216, "T", "A", "POLQ", 77.6, "LowQual"),
    ("chr3", 121168216, "T", "C", "POLQ", 81.1, "PASS"),
    ("chr3", 121179033, "A", "G", "POLQ", 98.4, "PASS"),
    ("chr3", 121186472, "C", "T", "POLQ", 82.5, "PASS"),
    ("chr3", 121187190, "A", "C", "POLQ", 62.7, "PASS"),
    ("chr3", 121187205, "T", "C", "POLQ", 54.7, "LowQual"),
    ("chr3", 121187214, "T", "G", "POLQ", 77.6, "PASS"),
    ("chr3", 121187248, "T", "G", "POLQ", 73.3, "PASS"),
    ("chr3", 121190841, "A", "G", "POLQ", 57.0, "PASS"),
    ("chr2", 179446430, "T", "C", "TTN-AS1", 54.7, "PASS"),
    ("chr2", 197066030, "C", "T", "HECW2", 56.3, "PASS"),
    ("chr2", 197084780, "T", "C", "HECW2", 64.7, "PASS"),
    ("chr2", 197084813, "G", "A", "HECW2", 61.3, "PASS"),
    ("chr2", 197090563, "C", "T", "HECW2", 95.7, "LowQual"),
    ("chr2", 197106902, "G", "A", "HECW2", 73.5, "PASS"),
    ("chr2", 179447099, "G", "A", "TTN-AS1", 78.5, "LowQual"),
    ("chr2", 197171856, "G", "A", "HECW2", 50.6, "PASS"),
    ("chr2", 197171883, "T", "G", "HECW2", 61.9, "PASS"),
    ("chr2", 179447175, "C", "T", "TTN-AS1", 86.9, "LowQual"),
    ("chr2", 197183348, "C", "G", "HECW2", 57.5, "LowQual"),
    ("chr2", 197183398, "C", "T", "HECW2", 75.3, "PASS"),
    ("chr2", 179447336, "G", "A", "TTN-AS1", 78.5, "PASS"),
    ("chr2", 179403801, "G", "A", "TTN-AS1", 75.5, "PASS"),
    ("chr2", 179403836, "G", "C", "TTN-AS1", 75.5, "PASS"),
    ("chr2", 179403932, "G", "A", "TTN-AS1", 61.9, "LowQual"),
    ("chr2", 197183618, "C", "T", "HECW2", 84.1, "PASS"),
    ("chr2", 179447686, "G", "T", "TTN-AS1", 81.8, "PASS"),
    ("chr2", 197183636, "A", "C", "HECW2", 77.5, "PASS"),
    ("chr2", 179447744, "T", "C", "TTN-AS1", 53.3, "PASS"),
    ("chr2", 197184063, "T", "G", "HECW2", 69.6, "LowQual"),
    ("chr2", 197184149, "T", "G", "HECW2", 78.2, "LowQual"),
    ("chr2", 179447864, "C", "A", "TTN-AS1", 79.9, "LowQual"),
    ("chr2", 197184521, "G", "C", "HECW2", 64.8, "PASS"),
    ("chr2", 179448381, "C", "T", "TTN-AS1", 77.4, "LowQual"),
    ("chr2", 197298066, "G", "A", "HECW2", 79.8, "PASS"),
    ("chr2", 179448642, "A", "C", "TTN-AS1", 60.6, "PASS"),
    ("chr2", 197559839, "A", "C", "CCDC150", 50.0, "PASS"),
    ("chr2", 197584281, "A", "G", "CCDC150", 76.3, "PASS"),
    ("chr2", 179449020, "G", "A", "TTN-AS1", 62.5, "PASS"),
    ("chr2", 179449072, "C", "A", "TTN-AS1", 93.5, "PASS"),
    ("chr3", 121206353, "A", "G", "POLQ", 60.8, "PASS"),
    ("chr3", 121206391, "T", "C", "POLQ", 91.6, "LowQual"),
    ("chr3", 121206442, "T", "A", "POLQ", 66.7, "PASS"),
    ("chr3", 121206458, "A", "T", "POLQ", 96.3, "LowQual"),
    ("chr3", 121206501, "A", "T", "POLQ", 67.3, "PASS"),
    ("chr3", 121206509, "C", "G", "POLQ", 90.2, "PASS"),
    ("chr3", 121206510, "A", "C", "POLQ", 65.0, "PASS"),
    ("chr2", 179391680, "C", "T", "TTN-AS1", 62.9, "PASS"),
    ("chr3", 121206525, "C", "G", "POLQ", 82.3, "LowQual"),
    ("chr3", 121206538, "A", "G", "POLQ", 97.5, "LowQual"),
    ("chr3", 121206617, "A", "C", "POLQ", 57.1, "PASS"),
    ("chr3", 121206710, "C", "T", "POLQ", 69.9, "PASS"),
    ("chr2", 179403974, "A", "G", "TTN-AS1", 67.4, "PASS"),
    ("chr2", 179404177, "G", "C", "TTN-AS1", 61.0, "PASS"),
    ("chr2", 179404188, "G", "A", "TTN-AS1", 69.6, "PASS"),
    ("chr2", 179404224, "C", "T", "TTN-AS1", 85.9, "LowQual"),
    ("chr2", 179404236, "A", "G", "TTN-AS1", 75.3, "PASS"),
    ("chr2", 179404248, "G", "A", "TTN-AS1", 64.1, "PASS"),
    ("chr2", 179404293, "G", "C", "TTN-AS1", 87.5, "PASS"),
    ("chr17", 41245203, "C", "A", "BRCA1", 59.0, "PASS"),
    ("chr17", 41245232, "T", "C", "BRCA1", 86.4, "PASS"),
    ("chr2", 179404584, "A", "G", "TTN-AS1", 59.2, "PASS"),
    ("chr2", 179404635, "A", "G", "TTN-AS1", 68.7, "PASS"),
    ("chr2", 179404820, "T", "A", "TTN-AS1", 55.8, "PASS"),
    ("chr17", 41245249, "T", "C", "BRCA1", 62.3, "PASS"),
    ("chr17", 41245253, "C", "T", "BRCA1", 68.9, "PASS"),
    ("chr17", 41245254, "T", "C", "BRCA1", 74.3, "PASS"),
    ("chr2", 179405093, "A", "C", "TTN-AS1", 56.2, "PASS"),
    ("chr17", 41245264, "T", "G", "BRCA1", 50.5, "PASS"),
    ("chr17", 41245266, "T", "A", "BRCA1", 63.8, "PASS"),
    ("chr2", 238243416, "G", "A", "COL6A3", 71.6, "LowQual"),
    ("chr2", 210808144, "C", "T", "UNC80", 96.5, "PASS"),
    ("chr2", 238243452, "C", "T", "COL6A3", 96.9, "PASS"),
    ("chr2", 210808188, "C", "A", "UNC80", 79.2, "PASS"),
    ("chr2", 210808218, "G", "A", "UNC80", 51.5, "PASS"),
    ("chr2", 210809792, "G", "A", "UNC80", 61.7, "LowQual"),
    ("chr2", 210809813, "T", "C", "UNC80", 71.5, "PASS"),
    ("chr2", 238243551, "C", "A", "COL6A3", 50.4, "PASS"),
    ("chr2", 238244769, "C", "T", "COL6A3", 78.5, "LowQual"),
    ("chr3", 123386048, "G", "A", "MYLK", 98.7, "PASS"),
    ("chr2", 238244963, "A", "G", "COL6A3", 97.0, "PASS"),
    ("chr3", 123401125, "C", "T", "MYLK", 62.4, "PASS"),
    ("chr3", 123401146, "T", "G", "MYLK", 59.7, "LowQual"),
    ("chr2", 238245109, "A", "G", "COL6A3", 97.9, "PASS"),
    ("chr3", 123411619, "A", "G", "MYLK", 74.0, "PASS"),
    ("chr2", 238245132, "C", "T", "COL6A3", 60.0, "PASS"),
    ("chr2", 210824311, "T", "C", "UNC80", 89.5, "PASS"),
    ("chr2", 202485965, "T", "C", "TMEM237", 64.0, "PASS"),
    ("chr2", 228563820, "C", "T", "SLC19A3", 64.1, "PASS"),
    ("chr2", 228563826, "T", "C", "SLC19A3", 71.5, "PASS"),
    ("chr2", 228563873, "G", "C", "SLC19A3", 63.6, "PASS"),
    ("chr2", 228563876, "A", "G", "SLC19A3", 57.3, "LowQual"),
    ("chr2", 47630236, "A", "T", "MSH2", 61.0, "PASS"),
    ("chr2", 228563927, "C", "T", "SLC19A3", 78.3, "LowQual"),
    ("chr2", 228563975, "T", "C", "SLC19A3", 57.1, "PASS"),
    ("chr2", 3196228, "C", "T", "EIPR1", 94.1, "LowQual"),
    ("chr2", 3196243, "C", "T", "EIPR1", 82.9, "LowQual"),
    ("chr2", 32312564, "G", "A", "SPAST", 84.0, "PASS"),
    ("chr2", 202492840, "C", "T", "TMEM237", 97.9, "PASS"),
    ("chr2", 47630308, "C", "T", "MSH2", 77.5, "PASS"),
    ("chr2", 202493971, "G", "A", "TMEM237", 69.7, "PASS"),
    ("chr2", 47630316, "T", "G", "MSH2", 87.8, "PASS"),
    ("chr2", 228564199, "G", "A", "SLC19A3", 87.7, "LowQual"),
    ("chr2", 202494351, "G", "C", "TMEM237", 51.7, "PASS"),
    ("chr2", 202494441, "A", "G", "TMEM237", 61.4, "PASS"),
    ("chr2", 228564287, "A", "G", "SLC19A3", 75.8, "PASS"),
    ("chr2", 228565742, "G", "C", "SLC19A3", 58.8, "PASS"),
    ("chr3", 11064029, "A", "G", "SLC6A1", 69.7, "LowQual"),
    ("chr2", 31598372, "C", "T", "XDH", 70.4, "LowQual"),
    ("chr3", 11067128, "C", "T", "SLC6A1", 57.3, "PASS"),
    ("chr3", 11067139, "T", "C", "SLC6A1", 86.0, "PASS"),
    ("chr2", 31600146, "T", "C", "XDH", 68.0, "PASS"),
    ("chr3", 11067167, "C", "A", "SLC6A1", 70.6, "PASS"),
    ("chr3", 11067199, "C", "T", "SLC6A1", 58.2, "PASS"),
    ("chr3", 11067209, "G", "T", "SLC6A1", 54.3, "PASS"),
    ("chr2", 179408802, "A", "C", "LOC126806421", 51.5, "LowQual"),
    ("chr3", 11067218, "G", "A", "SLC6A1", 77.4, "PASS"),
    ("chr3", 11067224, "C", "T", "SLC6A1", 88.9, "PASS"),
    ("chr3", 11067257, "G", "A", "SLC6A1", 91.0, "PASS"),
    ("chr2", 31605994, "G", "A", "XDH", 92.8, "LowQual"),
    ("chr2", 31606616, "C", "T", "XDH", 68.5, "LowQual"),
    ("chr2", 179408964, "C", "A", "TTN-AS1", 76.7, "PASS"),
    ("chr3", 11067513, "T", "A", "SLC6A1", 72.3, "LowQual"),
    ("chr2", 179409182, "C", "T", "TTN-AS1", 52.5, "LowQual"),
    ("chr2", 179409184, "G", "T", "TTN-AS1", 83.3, "PASS"),
    ("chr2", 179409190, "G", "T", "TTN-AS1", 86.9, "LowQual"),
    ("chr2", 179410097, "A", "G", "TTN-AS1", 60.6, "PASS"),
    ("chr2", 179410112, "C", "A", "TTN-AS1", 98.5, "PASS"),
    ("chr3", 11067928, "A", "G", "SLC6A1", 90.6, "PASS"),
    ("chr2", 31609416, "C", "T", "XDH", 66.8, "PASS"),
    ("chr17", 41244448, "T", "C", "BRCA1", 64.2, "PASS"),
    ("chr3", 121208703, "C", "T", "POLQ", 87.4, "LowQual"),
    ("chr2", 179394212, "G", "A", "TTN-AS1", 53.2, "PASS"),
    ("chr2", 179394704, "C", "T", "TTN-AS1", 99.5, "PASS"),
    ("chr3", 121208754, "C", "G", "POLQ", 72.4, "PASS"),
    ("chr2", 179394797, "C", "G", "TTN-AS1", 90.3, "PASS"),
    ("chr3", 121208858, "G", "C", "POLQ", 69.9, "LowQual"),
    ("chr2", 179395030, "T", "C", "TTN-AS1", 74.1, "PASS"),
    ("chr2", 179395070, "A", "T", "TTN-AS1", 91.9, "PASS"),
    ("chr3", 121209033, "C", "T", "POLQ", 52.9, "PASS"),
    ("chr3", 121209055, "G", "A", "POLQ", 62.5, "PASS"),
    ("chr2", 179395112, "T", "G", "TTN-AS1", 50.9, "PASS"),
    ("chr2", 232952428, "A", "G", "DIS3L2", 50.8, "PASS"),
    ("chr2", 204037528, "A", "G", "NBEAL1", 86.2, "PASS"),
    ("chr2", 20403836, "G", "T", "SDC1", 92.2, "PASS"),
    ("chr3", 121712239, "G", "A", "ILDR1", 67.0, "PASS"),
    ("chr2", 20405173, "T", "C", "SDC1", 69.4, "PASS"),
    ("chr2", 32503238, "G", "T", "YIPF4", 98.2, "PASS"),
    ("chr2", 232995368, "C", "A", "DIS3L2", 78.2, "LowQual"),
    ("chr2", 47641478, "A", "G", "MSH2", 59.5, "PASS"),
    ("chr2", 204058598, "T", "G", "NBEAL1", 85.2, "PASS"),
    ("chr2", 204073435, "G", "A", "NBEAL1", 75.7, "PASS"),
    ("chr2", 232995432, "C", "A", "DIS3L2", 98.5, "PASS"),
    ("chr2", 47641490, "C", "T", "MSH2", 81.4, "PASS"),
    ("chr2", 32613972, "G", "A", "BIRC6", 58.3, "PASS"),
    ("chr2", 47641502, "T", "A", "MSH2", 95.6, "PASS"),
    ("chr2", 32640322, "A", "C", "BIRC6", 96.9, "PASS"),
    ("chr2", 233001213, "G", "A", "DIS3L2", 93.2, "PASS"),
    ("chr2", 179395299, "T", "G", "LOC129935182", 57.3, "PASS"),
    ("chr2", 179395302, "T", "C", "LOC129935182", 81.4, "PASS"),
    ("chr17", 41244515, "T", "C", "BRCA1", 61.4, "PASS"),
    ("chr2", 179395390, "T", "A", "LOC129935183", 86.3, "LowQual"),
    ("chr2", 179395491, "G", "C", "LOC129935183", 74.5, "PASS"),
    ("chr3", 121209254, "C", "T", "POLQ", 88.1, "PASS"),
    ("chr3", 121212360, "C", "T", "POLQ", 99.0, "PASS"),
    ("chr3", 121212379, "C", "T", "POLQ", 71.2, "PASS"),
    ("chr3", 121212489, "C", "T", "POLQ", 56.9, "PASS"),
    ("chr3", 121212567, "C", "G", "POLQ", 85.1, "PASS"),
    ("chr2", 179395611, "G", "A", "LOC129935183", 88.7, "PASS"),
    ("chr3", 121215700, "G", "A", "POLQ", 76.9, "PASS"),
    ("chr17", 41244540, "A", "G", "BRCA1", 54.2, "PASS"),
    ("chr3", 121215745, "T", "C", "POLQ", 64.6, "PASS"),
    ("chr2", 210849594, "T", "G", "UNC80", 76.9, "LowQual"),
    ("chr3", 123419717, "G", "A", "MYLK", 90.3, "PASS"),
    ("chr2", 48018129, "T", "C", "MSH6", 80.3, "LowQual"),
    ("chr2", 48018130, "C", "G", "MSH6", 97.0, "PASS"),
    ("chr2", 210858022, "C", "T", "UNC80", 82.0, "LowQual"),
    ("chr2", 210858035, "T", "C", "UNC80", 75.4, "PASS"),
    ("chr2", 42883441, "C", "T", "MTA3", 93.6, "PASS"),
    ("chr2", 210858051, "C", "G", "UNC80", 56.6, "PASS"),
    ("chr2", 210858075, "A", "G", "UNC80", 90.2, "PASS"),
    ("chr2", 238253331, "G", "A", "COL6A3", 71.1, "PASS"),
    ("chr2", 210858102, "C", "G", "UNC80", 59.4, "PASS"),
    ("chr3", 123419823, "A", "C", "MYLK", 66.0, "PASS"),
    ("chr2", 42936201, "T", "G", "MTA3", 55.0, "PASS"),
    ("chr2", 48018144, "C", "T", "MSH6", 61.1, "PASS"),
    ("chr2", 210858774, "C", "G", "UNC80", 52.2, "LowQual"),
    ("chr2", 238253395, "T", "G", "COL6A3", 99.2, "PASS"),
    ("chr2", 210858802, "A", "G", "UNC80", 67.3, "PASS"),
    ("chr2", 210858835, "A", "T", "UNC80", 82.0, "LowQual"),
    ("chr2", 210858877, "A", "G", "UNC80", 70.5, "PASS"),
    ("chr2", 210858888, "G", "A", "UNC80", 72.1, "PASS"),
    ("chr3", 111451471, "G", "A", "PLCXD2", 67.9, "LowQual"),
    ("chr3", 111697987, "C", "T", "ABHD10", 61.0, "PASS"),
    ("chr3", 111710243, "T", "C", "ABHD10", 71.6, "PASS"),
    ("chr3", 111760859, "A", "G", "TMPRSS7", 64.0, "PASS"),
    ("chr3", 111766665, "G", "T", "TMPRSS7", 64.0, "LowQual"),
    ("chr3", 111768779, "C", "T", "TMPRSS7", 63.6, "PASS"),
    ("chr3", 111793236, "A", "T", "TMPRSS7", 58.0, "PASS"),
    ("chr3", 111794230, "G", "T", "TMPRSS7", 84.0, "PASS"),
    ("chr3", 111835712, "A", "G", "C3orf52", 72.5, "LowQual"),
    ("chr3", 111993749, "G", "A", "SLC9C1", 82.6, "PASS"),
    ("chr3", 111993788, "A", "G", "SLC9C1", 55.7, "PASS"),
    ("chr3", 112054858, "T", "A", "CD200", 78.0, "LowQual"),
    ("chr3", 112256712, "A", "C", "ATG3", 75.9, "PASS"),
    ("chr3", 112299424, "C", "T", "SLC35A5", 70.5, "PASS"),
    ("chr2", 202617969, "A", "T", "ALS2", 84.4, "PASS"),
    ("chr2", 231033907, "T", "C", "SP110", 87.6, "PASS"),
    ("chr2", 47630650, "G", "A", "MSH2", 90.5, "PASS"),
    ("chr2", 47630655, "C", "T", "MSH2", 53.9, "LowQual"),
    ("chr2", 231035410, "G", "A", "SP110", 58.5, "PASS"),
    ("chr2", 231035466, "G", "A", "SP110", 97.3, "LowQual"),
    ("chr2", 202622306, "A", "G", "ALS2", 74.6, "PASS"),
    ("chr2", 47635530, "T", "C", "MSH2", 85.2, "LowQual"),
    ("chr2", 231036906, "C", "G", "SP110", 70.9, "PASS"),
    ("chr3", 121305316, "G", "A", "ARGFX", 61.2, "LowQual"),
    ("chr2", 202622509, "T", "C", "ALS2", 69.4, "PASS"),
    ("chr2", 202625608, "G", "A", "ALS2", 52.5, "LowQual"),
    ("chr2", 202625706, "T", "C", "ALS2", 87.0, "PASS"),
    ("chr2", 231042297, "C", "T", "SP110", 50.6, "PASS"),
    ("chr2", 32351997, "C", "A", "SPAST", 91.7, "PASS"),
    ("chr2", 233001443, "G", "C", "DIS3L2", 58.2, "LowQual"),
    ("chr2", 233028162, "T", "C", "DIS3L2", 77.8, "PASS"),
    ("chr2", 32702639, "G", "T", "BIRC6", 71.2, "PASS"),
    ("chr2", 233028172, "G", "A", "DIS3L2", 93.6, "LowQual"),
    ("chr2", 204360053, "T", "G", "RAPH1", 64.2, "PASS"),
    ("chr3", 121725821, "G", "T", "ILDR1", 53.8, "PASS"),
    ("chr2", 32718615, "T", "C", "BIRC6", 89.3, "LowQual"),
    ("chr2", 32724799, "G", "A", "BIRC6", 92.4, "PASS"),
    ("chr2", 204732695, "G", "A", "CTLA4", 96.2, "LowQual"),
    ("chr2", 204732727, "C", "G", "CTLA4", 71.8, "PASS"),
    ("chr2", 233028277, "A", "G", "DIS3L2", 77.1, "PASS"),
    ("chr3", 112357162, "G", "A", "CCDC80", 64.2, "PASS"),
    ("chr3", 112357707, "C", "G", "CCDC80", 86.5, "PASS"),
    ("chr3", 112358008, "G", "C", "CCDC80", 51.1, "LowQual"),
    ("chr3", 112545865, "C", "G", "CD200R1L", 62.3, "LowQual"),
    ("chr3", 112989764, "G", "A", "BOC", 81.5, "PASS"),
    ("chr3", 112993431, "C", "T", "BOC", 84.4, "PASS"),
    ("chr3", 112997546, "G", "A", "BOC", 87.0, "PASS"),
    ("chr3", 113084918, "T", "C", "SPICE1-CFAP44", 86.0, "PASS"),
    ("chr3", 113092306, "C", "T", "SPICE1-CFAP44", 67.8, "PASS"),
    ("chr3", 113125794, "T", "C", "CFAP44-AS1", 52.5, "PASS"),
    ("chr3", 113125841, "G", "A", "CFAP44-AS1", 65.1, "PASS"),
    ("chr2", 231042868, "C", "T", "SP110", 62.6, "PASS"),
    ("chr2", 202625933, "T", "C", "ALS2", 99.8, "LowQual"),
    ("chr2", 231042893, "T", "C", "SP110", 56.6, "PASS"),
    ("chr2", 207631480, "G", "A", "FASTKD2", 57.9, "PASS"),
    ("chr2", 202626071, "G", "C", "ALS2", 54.3, "LowQual"),
    ("chr2", 231048366, "G", "C", "SP110", 98.6, "PASS"),
    ("chr2", 231050788, "C", "T", "SP110", 66.0, "LowQual"),
    ("chr2", 202626386, "C", "T", "ALS2", 76.6, "PASS"),
    ("chr2", 202626432, "A", "C", "ALS2", 97.6, "LowQual"),
    ("chr2", 231050867, "A", "G", "SP110", 82.2, "PASS"),
    ("chr2", 207631614, "A", "G", "FASTKD2", 83.1, "LowQual"),
    ("chr2", 233396170, "G", "A", "CHRND", 68.6, "PASS"),
    ("chr2", 37374068, "T", "C", "EIF2AK2", 65.6, "PASS"),
    ("chr3", 121350767, "C", "G", "HCLS1", 50.5, "LowQual"),
    ("chr2", 47635573, "A", "T", "MSH2", 75.7, "PASS"),
    ("chr2", 231067306, "G", "A", "SP110", 71.3, "PASS"),
    ("chr2", 47635578, "A", "C", "MSH2", 83.4, "LowQual"),
    ("chr2", 32734915, "C", "G", "BIRC6", 90.0, "LowQual"),
    ("chr2", 32735633, "C", "G", "BIRC6", 52.9, "PASS"),
    ("chr3", 121828115, "T", "C", "CD86", 83.1, "PASS"),
    ("chr2", 204735316, "C", "T", "CTLA4", 89.8, "PASS"),
    ("chr3", 121828238, "G", "A", "CD86", 73.7, "LowQual"),
    ("chr2", 233028348, "C", "T", "DIS3L2", 94.9, "PASS"),
    ("chr3", 121838322, "C", "G", "CD86", 77.0, "PASS"),
    ("chr2", 233028351, "C", "G", "DIS3L2", 73.1, "PASS"),
    ("chr2", 32740492, "T", "A", "BIRC6", 68.9, "PASS"),
    ("chr2", 47643443, "T", "C", "MSH2", 87.3, "PASS"),
    ("chr3", 12187229, "C", "T", "SYN2", 90.7, "PASS"),
    ("chr2", 47643447, "G", "T", "MSH2", 92.0, "PASS"),
    ("chr2", 32743369, "A", "G", "BIRC6", 66.7, "PASS"),
    ("chr2", 47643452, "C", "G", "MSH2", 68.3, "PASS"),
    ("chr2", 32754769, "A", "G", "BIRC6", 91.4, "PASS"),
    ("chr3", 121973037, "A", "C", "CASR", 51.9, "PASS"),
    ("chr2", 204735462, "C", "A", "CTLA4", 63.5, "PASS"),
    ("chr2", 233075105, "A", "G", "DIS3L2", 66.9, "PASS"),
    ("chr2", 233075124, "G", "A", "DIS3L2", 80.3, "PASS"),
    ("chr2", 233075131, "C", "T", "DIS3L2", 80.1, "PASS"),
    ("chr2", 204735551, "G", "C", "CTLA4", 83.9, "PASS"),
    ("chr2", 179416874, "A", "G", "TTN-AS1", 52.4, "LowQual"),
    ("chr2", 179417097, "A", "C", "TTN-AS1", 88.4, "PASS"),
    ("chr2", 179417789, "A", "G", "TTN-AS1", 83.1, "PASS"),
    ("chr3", 113172709, "C", "A", "SPICE1-CFAP44", 58.1, "LowQual"),
    ("chr2", 179418444, "C", "T", "TTN-AS1", 68.5, "PASS"),
    ("chr3", 113321990, "G", "T", "SIDT1", 97.9, "PASS"),
    ("chr3", 113329893, "C", "A", "SIDT1", 82.4, "PASS"),
    ("chr3", 113373808, "A", "C", "USF3", 98.8, "PASS"),
    ("chr3", 113374618, "T", "C", "USF3", 71.8, "LowQual"),
    ("chr3", 113375125, "T", "C", "USF3", 98.1, "PASS"),
    ("chr3", 113376684, "T", "C", "USF3", 58.7, "PASS"),
    ("chr3", 113376724, "C", "T", "USF3", 86.2, "PASS"),
    ("chr3", 113376977, "A", "T", "USF3", 56.1, "LowQual"),
    ("chr3", 113379783, "A", "C", "USF3", 73.8, "LowQual"),
    ("chr3", 113497631, "G", "T", "ATP6V1A", 52.3, "PASS"),
    ("chr3", 113497665, "A", "G", "ATP6V1A", 68.7, "PASS"),
    ("chr3", 113499940, "G", "A", "ATP6V1A", 90.2, "LowQual"),
    ("chr3", 113503058, "C", "T", "ATP6V1A", 61.4, "PASS"),
    ("chr3", 113503112, "C", "A", "ATP6V1A", 56.1, "LowQual"),
    ("chr3", 113503158, "A", "T", "ATP6V1A", 64.0, "PASS"),
    ("chr3", 113503177, "G", "A", "ATP6V1A", 58.5, "PASS"),
    ("chr3", 121240956, "T", "C", "POLQ", 55.5, "PASS"),
    ("chr2", 179396625, "T", "A", "TTN-AS1", 80.3, "PASS"),
    ("chr2", 179396629, "A", "G", "TTN-AS1", 84.1, "PASS"),
    ("chr2", 179396681, "G", "T", "TTN-AS1", 97.3, "PASS"),
    ("chr3", 121248620, "A", "C", "POLQ", 53.8, "PASS"),
    ("chr2", 202632352, "G", "A", "ALS2", 50.0, "PASS"),
    ("chr2", 32353500, "G", "A", "SPAST", 99.9, "PASS"),
    ("chr2", 202755561, "C", "A", "CDK15", 53.0, "PASS"),
    ("chr2", 231077112, "G", "T", "SP110", 91.0, "PASS"),
    ("chr3", 121366255, "C", "T", "HCLS1", 86.8, "PASS"),
    ("chr2", 47635603, "T", "C", "MSH2", 80.3, "PASS"),
    ("chr2", 32361636, "G", "C", "SPAST", 61.2, "PASS"),
    ("chr2", 47635605, "C", "G", "MSH2", 76.1, "PASS"),
    ("chr2", 231077652, "G", "A", "SP110", 60.1, "LowQual"),
    ("chr3", 121973100, "C", "T", "CASR", 76.5, "PASS"),
    ("chr2", 233103320, "G", "T", "DIS3L2", 81.3, "PASS"),
    ("chr2", 233103323, "G", "A", "DIS3L2", 57.9, "PASS"),
    ("chr2", 32891752, "A", "G", "TTC27", 61.8, "PASS"),
    ("chr2", 233103342, "A", "G", "DIS3L2", 83.8, "PASS"),
    ("chr3", 121973122, "A", "G", "CASR", 51.2, "PASS"),
    ("chr2", 32961801, "G", "C", "TTC27", 61.9, "PASS"),
    ("chr2", 32983497, "C", "T", "TTC27", 79.0, "LowQual"),
    ("chr2", 233113995, "T", "C", "DIS3L2", 96.1, "PASS"),
    ("chr2", 33173962, "G", "A", "LTBP1", 93.1, "PASS"),
    ("chr3", 122002736, "C", "T", "CASR", 83.6, "PASS"),
    ("chr2", 47698171, "A", "G", "MSH2", 55.7, "LowQual"),
    ("chr2", 207636927, "A", "G", "FASTKD2", 55.7, "LowQual"),
    ("chr2", 207636977, "A", "G", "FASTKD2", 95.1, "PASS"),
    ("chr2", 233399904, "C", "G", "CHRND", 66.9, "PASS"),
    ("chr3", 122002781, "C", "T", "CASR", 50.6, "PASS"),
    ("chr2", 233399991, "C", "G", "CHRND", 63.2, "PASS"),
    ("chr2", 37459260, "A", "G", "LOC126806192", 91.8, "PASS"),
    ("chr2", 207651606, "G", "A", "FASTKD2", 50.8, "PASS"),
    ("chr2", 37464884, "T", "A", "NDUFAF7", 92.1, "PASS"),
    ("chr2", 233400569, "G", "C", "CHRNG", 72.4, "PASS"),
    ("chr2", 37464947, "C", "T", "NDUFAF7", 78.2, "LowQual"),
    ("chr2", 207652696, "G", "A", "FASTKD2", 81.4, "PASS"),
    ("chr2", 47698217, "C", "A", "MSH2", 81.3, "PASS"),
    ("chr3", 127325449, "G", "A", "MCM2", 62.8, "PASS"),
    ("chr3", 123441107, "G", "A", "MYLK", 64.3, "PASS"),
    ("chr3", 127325516, "G", "T", "MCM2", 85.4, "LowQual"),
    ("chr3", 127327309, "G", "A", "MCM2", 74.3, "PASS"),
    ("chr2", 48023065, "C", "T", "MSH6", 66.6, "PASS"),
    ("chr17", 41245472, "A", "G", "BRCA1", 91.0, "PASS"),
    ("chr3", 123444937, "A", "C", "MYLK", 80.6, "LowQual"),
    ("chr2", 43783558, "G", "A", "THADA", 63.1, "PASS"),
    ("chr3", 123451773, "G", "C", "MYLK", 57.7, "PASS"),
    ("chr3", 127335841, "G", "A", "MCM2", 87.9, "PASS"),
    ("chr2", 179422765, "C", "A", "TTN-AS1", 51.1, "PASS"),
    ("chr2", 179423180, "A", "G", "TTN-AS1", 82.4, "PASS"),
    ("chr2", 179423252, "G", "A", "TTN-AS1", 64.2, "PASS"),
    ("chr2", 179423335, "C", "G", "TTN-AS1", 84.0, "PASS"),
    ("chr2", 179423366, "T", "C", "TTN-AS1", 92.2, "PASS"),
    ("chr2", 179424048, "T", "C", "TTN-AS1", 61.8, "PASS"),
    ("chr2", 179424246, "G", "A", "TTN-AS1", 53.7, "PASS"),
    ("chr2", 179424514, "G", "A", "TTN-AS1", 61.0, "LowQual"),
    ("chr2", 179424966, "A", "G", "TTN-AS1", 71.1, "PASS"),
    ("chr2", 48023106, "A", "T", "MSH6", 85.2, "PASS"),
    ("chr2", 48023115, "T", "A", "MSH6", 71.1, "PASS"),
    ("chr3", 127337926, "C", "G", "MCM2", 78.8, "LowQual"),
    ("chr2", 43808973, "C", "A", "THADA", 62.1, "PASS"),
    ("chr2", 211421460, "G", "T", "CPS1", 73.5, "LowQual"),
    ("chr2", 211421463, "G", "A", "CPS1", 74.6, "LowQual"),
    ("chr2", 48023139, "T", "G", "MSH6", 55.1, "PASS"),
    ("chr3", 123452604, "G", "A", "MYLK", 97.0, "PASS"),
    ("chr2", 43902723, "G", "T", "C1GALT1C1L", 77.4, "PASS"),
    ("chr2", 238266481, "T", "G", "COL6A3", 84.5, "PASS"),
    ("chr2", 43903091, "T", "G", "C1GALT1C1L", 96.4, "PASS"),
    ("chr2", 179425248, "T", "G", "TTN-AS1", 53.5, "LowQual"),
    ("chr2", 179425324, "A", "G", "TTN-AS1", 75.5, "LowQual"),
    ("chr2", 179425345, "A", "C", "TTN-AS1", 84.7, "PASS"),
    ("chr2", 179425611, "T", "A", "TTN-AS1", 52.1, "PASS"),
    ("chr2", 179426682, "T", "C", "TTN-AS1", 80.1, "PASS"),
    ("chr2", 179426706, "A", "G", "TTN-AS1", 88.2, "LowQual"),
    ("chr2", 17942676, "C", "T", "GEN1", 71.6, "PASS"),
    ("chr2", 179426920, "A", "G", "TTN-AS1", 98.7, "LowQual"),
    ("chr2", 179426934, "C", "T", "TTN-AS1", 57.2, "PASS"),
    ("chr2", 43903136, "A", "G", "C1GALT1C1L", 81.3, "LowQual"),
    ("chr3", 123452690, "T", "C", "MYLK", 52.0, "PASS"),
    ("chr2", 211438042, "C", "G", "CPS1", 57.8, "PASS"),
    ("chr2", 48023181, "A", "T", "MSH6", 53.1, "LowQual"),
    ("chr3", 127340074, "A", "G", "MCM2", 51.0, "PASS"),
    ("chr2", 43931125, "C", "A", "PLEKHH2", 93.9, "PASS"),
    ("chr2", 204821388, "A", "C", "ICOS", 64.3, "PASS"),
    ("chr3", 123452818, "G", "C", "MYLK", 98.4, "LowQual"),
    ("chr2", 48023196, "G", "A", "MSH6", 99.5, "PASS"),
    ("chr2", 238267741, "A", "G", "COL6A3", 68.6, "PASS"),
    ("chr2", 233194576, "A", "G", "DIS3L2", 62.4, "PASS"),
    ("chr2", 233408294, "G", "A", "CHRNG", 96.8, "PASS"),
    ("chr2", 233408404, "C", "T", "CHRNG", 71.8, "PASS"),
    ("chr2", 233408419, "C", "G", "CHRNG", 67.8, "PASS"),
    ("chr2", 208486553, "A", "T", "METTL21A", 72.9, "PASS"),
    ("chr2", 233409100, "G", "A", "CHRNG", 79.3, "PASS"),
    ("chr2", 38297994, "C", "T", "CYP1B1", 56.9, "LowQual"),
    ("chr2", 47702268, "C", "G", "MSH2", 97.3, "LowQual"),
    ("chr2", 38297997, "A", "T", "CYP1B1", 77.4, "PASS"),
    ("chr2", 38298038, "G", "A", "CYP1B1", 94.0, "PASS"),
    ("chr3", 122003190, "C", "A", "CASR", 61.1, "PASS"),
    ("chr2", 208631783, "C", "A", "FZD5", 50.5, "LowQual"),
    ("chr2", 208631784, "G", "A", "FZD5", 68.5, "PASS"),
    ("chr2", 233409188, "A", "G", "CHRNG", 52.8, "PASS"),
    ("chr3", 122003226, "T", "A", "CASR", 67.5, "PASS"),
    ("chr2", 38298175, "T", "C", "CYP1B1", 92.9, "LowQual"),
    ("chr2", 179428933, "C", "T", "TTN-AS1", 92.6, "PASS"),
    ("chr2", 179428937, "C", "T", "TTN-AS1", 68.7, "PASS"),
    ("chr2", 179428954, "T", "C", "TTN-AS1", 93.3, "PASS"),
    ("chr2", 179428978, "A", "C", "TTN-AS1", 61.7, "PASS"),
    ("chr2", 179429106, "A", "G", "TTN-AS1", 64.4, "PASS"),
    ("chr2", 179429122, "A", "G", "TTN-AS1", 86.7, "PASS"),
    ("chr2", 179429250, "T", "C", "TTN-AS1", 55.6, "PASS"),
    ("chr2", 179429376, "C", "T", "TTN-AS1", 99.8, "PASS"),
    ("chr2", 179429544, "A", "G", "TTN-AS1", 96.5, "LowQual"),
    ("chr2", 179429667, "A", "G", "TTN-AS1", 53.3, "LowQual"),
    ("chr2", 179429726, "A", "G", "TTN-AS1", 83.6, "PASS"),
    ("chr2", 179429862, "A", "T", "TTN-AS1", 59.5, "PASS"),
    ("chr2", 179429886, "G", "C", "TTN-AS1", 94.3, "LowQual"),
    ("chr2", 179429915, "A", "G", "TTN-AS1", 73.2, "PASS"),
    ("chr2", 179429917, "C", "T", "TTN-AS1", 60.1, "PASS"),
    ("chr2", 179429918, "G", "A", "TTN-AS1", 71.9, "PASS"),
    ("chr2", 179430024, "A", "G", "TTN-AS1", 76.9, "PASS"),
    ("chr2", 179430039, "T", "C", "TTN-AS1", 89.8, "PASS"),
    ("chr2", 179430042, "A", "C", "TTN-AS1", 82.3, "PASS"),
    ("chr2", 179430155, "G", "A", "TTN-AS1", 55.9, "PASS"),
    ("chr2", 17943015, "T", "C", "GEN1", 76.5, "PASS"),
    ("chr2", 48025755, "C", "G", "MSH6", 78.3, "LowQual"),
    ("chr17", 41245579, "G", "C", "BRCA1", 70.7, "PASS"),
    ("chr3", 127390334, "C", "G", "PODXL2", 63.7, "LowQual"),
    ("chr3", 123456209, "G", "A", "MYLK", 97.8, "PASS"),
    ("chr2", 48025765, "G", "A", "MSH6", 64.1, "PASS"),
    ("chr2", 238274601, "A", "G", "COL6A3", 76.4, "PASS"),
    ("chr2", 211459220, "A", "G", "CPS1", 73.5, "LowQual"),
    ("chr2", 211459227, "T", "C", "CPS1", 93.9, "PASS"),
    ("chr3", 123456273, "C", "T", "MYLK", 79.2, "PASS"),
    ("chr2", 48025777, "A", "T", "MSH6", 72.6, "PASS"),
    ("chr2", 44021766, "T", "C", "DYNC2LI1", 79.0, "PASS"),
    ("chr3", 123456339, "C", "T", "MYLK", 76.2, "PASS"),
    ("chr2", 38302013, "C", "T", "CYP1B1", 62.3, "PASS"),
    ("chr2", 233633275, "A", "G", "GIGYF2", 55.7, "PASS"),
    ("chr3", 122003451, "G", "T", "CASR", 67.4, "PASS"),
    ("chr2", 208989274, "A", "G", "CRYGD", 50.2, "PASS"),
    ("chr2", 208992949, "C", "T", "CRYGC", 78.1, "PASS"),
    ("chr2", 233633363, "T", "C", "GIGYF2", 71.9, "LowQual"),
    ("chr2", 208992994, "C", "T", "CRYGC", 90.9, "LowQual"),
    ("chr2", 47702390, "G", "T", "MSH2", 96.3, "LowQual"),
    ("chr3", 122003472, "C", "T", "CASR", 61.5, "PASS"),
    ("chr2", 233633420, "G", "A", "GIGYF2", 79.8, "LowQual"),
    ("chr2", 47702393, "G", "A", "MSH2", 87.6, "PASS"),
    ("chr2", 233633455, "C", "T", "GIGYF2", 56.0, "PASS"),
    ("chr2", 38302224, "A", "C", "CYP1B1", 65.8, "LowQual"),
    ("chr2", 233635642, "A", "G", "GIGYF2", 72.3, "LowQual"),
    ("chr2", 47702409, "G", "C", "MSH2", 66.2, "LowQual"),
    ("chr2", 38302337, "C", "G", "CYP1B1", 67.8, "PASS"),
    ("chr2", 233635882, "A", "G", "GIGYF2", 54.9, "PASS"),
    ("chr2", 38302362, "C", "T", "CYP1B1", 54.6, "PASS"),
    ("chr3", 123456371, "G", "T", "MYLK", 51.4, "LowQual"),
    ("chr3", 127395230, "A", "G", "ABTB1", 70.5, "LowQual"),
    ("chr2", 44023085, "T", "C", "DYNC2LI1", 57.9, "PASS"),
    ("chr2", 44023873, "A", "C", "DYNC2LI1", 84.0, "LowQual"),
    ("chr3", 123456397, "A", "G", "MYLK", 88.1, "PASS"),
    ("chr2", 48025805, "A", "T", "MSH6", 51.5, "LowQual"),
    ("chr2", 44027973, "T", "C", "DYNC2LI1", 74.4, "PASS"),
    ("chr2", 238275474, "C", "T", "COL6A3", 80.5, "LowQual"),
    ("chr2", 211460325, "T", "C", "CPS1", 50.7, "PASS"),
    ("chr3", 127396065, "C", "T", "ABTB1", 55.8, "PASS"),
    ("chr2", 44028034, "T", "C", "DYNC2LI1", 88.0, "PASS"),
    ("chr2", 179432255, "T", "G", "TTN-AS1", 61.2, "PASS"),
    ("chr2", 179432385, "T", "C", "TTN-AS1", 98.3, "PASS"),
    ("chr2", 179432386, "C", "G", "TTN-AS1", 83.4, "PASS"),
    ("chr2", 203420587, "G", "C", "BMPR2", 57.7, "LowQual"),
    ("chr2", 232234699, "C", "T", "ARMC9", 51.4, "PASS"),
    ("chr2", 203420635, "G", "A", "BMPR2", 99.1, "PASS"),
    ("chr2", 47637484, "T", "C", "MSH2", 63.3, "PASS"),
    ("chr2", 47637497, "G", "A", "MSH2", 56.7, "LowQual"),
    ("chr2", 232262782, "C", "T", "LOC126806551", 76.3, "PASS"),
    ("chr3", 121514338, "G", "C", "IQCB1", 63.5, "PASS"),
    ("chr2", 32474677, "C", "T", "NLRC4", 59.8, "LowQual"),
    ("chr2", 47637505, "G", "C", "MSH2", 52.6, "PASS"),
    ("chr2", 32474729, "A", "G", "NLRC4", 56.8, "PASS"),
    ("chr2", 232324919, "G", "A", "NCL", 86.9, "PASS"),
    ("chr2", 232326270, "G", "A", "NCL", 50.9, "PASS"),
    ("chr2", 179455168, "C", "T", "TTN-AS1", 67.4, "LowQual"),
    ("chr2", 179455201, "T", "C", "TTN-AS1", 81.9, "LowQual"),
    ("chr2", 199011526, "A", "G", "PLCL1", 51.2, "PASS"),
    ("chr2", 179455289, "G", "C", "TTN-AS1", 50.0, "LowQual"),
    ("chr2", 200136946, "A", "T", "LOC126806462", 53.0, "LowQual"),
    ("chr2", 200136962, "G", "A", "LOC126806462", 98.0, "PASS"),
    ("chr2", 200136975, "C", "T", "LOC126806462", 84.7, "PASS"),
    ("chr2", 179455636, "C", "T", "TTN-AS1", 62.9, "PASS"),
    ("chr2", 179455637, "G", "A", "TTN-AS1", 70.2, "LowQual"),
    ("chr2", 179455666, "A", "G", "TTN-AS1", 92.4, "PASS"),
    ("chr2", 200137362, "C", "T", "LOC126806462", 54.2, "PASS"),
    ("chr2", 200137375, "A", "G", "LOC126806462", 81.4, "PASS"),
    ("chr2", 179455902, "C", "T", "TTN-AS1", 97.3, "PASS"),
    ("chr2", 233756177, "C", "G", "NGEF", 76.9, "PASS"),
    ("chr2", 47703551, "T", "C", "MSH2", 75.1, "LowQual"),
    ("chr2", 47703553, "A", "G", "MSH2", 65.9, "PASS"),
    ("chr2", 38960661, "G", "A", "GALM", 79.2, "PASS"),
    ("chr2", 38960823, "A", "G", "GALM", 58.4, "LowQual"),
    ("chr2", 209106731, "G", "A", "IDH1", 66.0, "LowQual"),
    ("chr2", 209106740, "C", "T", "IDH1", 73.1, "PASS"),
    ("chr2", 209106769, "A", "G", "IDH1", 82.5, "PASS"),
    ("chr2", 233899179, "C", "A", "NEU2", 81.2, "PASS"),
    ("chr2", 39224031, "T", "C", "SOS1", 90.2, "PASS"),
    ("chr2", 39224063, "A", "T", "SOS1", 65.2, "PASS"),
    ("chr3", 122943951, "T", "A", "SEC22A", 70.3, "PASS"),
    ("chr2", 39224146, "T", "A", "SOS1", 71.8, "LowQual"),
    ("chr3", 122944137, "T", "G", "SEC22A", 76.0, "PASS"),
    ("chr2", 234591219, "G", "T", "UGT1A", 97.8, "PASS"),
    ("chr2", 47705613, "C", "T", "MSH2", 85.2, "PASS"),
    ("chr3", 123003499, "C", "T", "ADCY5", 53.4, "PASS"),
    ("chr3", 123003500, "G", "T", "ADCY5", 59.1, "LowQual"),
    ("chr2", 234591436, "A", "G", "UGT1A", 52.0, "PASS"),
    ("chr2", 39224409, "T", "C", "SOS1", 74.7, "PASS"),
    ("chr3", 123003553, "C", "T", "ADCY5", 63.1, "LowQual"),
    ("chr3", 123005513, "T", "C", "ADCY5", 94.1, "LowQual"),
    ("chr2", 210637830, "G", "A", "UNC80", 82.9, "PASS"),
    ("chr2", 210637851, "T", "C", "UNC80", 94.5, "PASS"),
    ("chr3", 123005605, "T", "G", "ADCY5", 61.4, "PASS"),
    ("chr2", 234601998, "G", "C", "UGT1A", 99.3, "LowQual"),
    ("chr2", 210640651, "C", "T", "UNC80", 78.6, "LowQual"),
    ("chr3", 123008605, "A", "G", "ADCY5", 68.5, "LowQual"),
    ("chr2", 47705648, "G", "A", "MSH2", 66.9, "PASS"),
    ("chr3", 123010097, "A", "G", "ADCY5", 74.5, "PASS"),
    ("chr2", 210642160, "G", "A", "UNC80", 82.9, "PASS"),
    ("chr2", 210642193, "A", "C", "UNC80", 50.0, "LowQual"),
    ("chr3", 123010228, "G", "A", "ADCY5", 92.4, "PASS"),
    ("chr2", 234628151, "G", "T", "UGT1A", 90.3, "PASS"),
    ("chr2", 39234235, "A", "G", "SOS1", 86.2, "PASS"),
    ("chr2", 210650813, "G", "T", "UNC80", 77.6, "PASS"),
    ("chr3", 123015012, "G", "A", "ADCY5", 84.4, "PASS"),
    ("chr2", 47707842, "T", "A", "MSH2", 98.4, "LowQual"),
    ("chr2", 234669128, "G", "A", "UGT1A", 59.3, "PASS"),
    ("chr2", 47707844, "A", "T", "MSH2", 80.8, "PASS"),
    ("chr3", 123021971, "G", "A", "ADCY5", 77.8, "PASS"),
    ("chr2", 210678359, "G", "A", "UNC80", 60.9, "LowQual"),
    ("chr2", 234669220, "G", "A", "UGT1A", 89.0, "LowQual"),
    ("chr2", 210678387, "C", "T", "UNC80", 55.5, "LowQual"),
    ("chr2", 210678394, "G", "A", "UNC80", 87.4, "PASS"),
    ("chr3", 121263707, "T", "C", "POLQ", 85.6, "PASS"),
    ("chr2", 179397598, "C", "G", "TTN-AS1", 92.1, "PASS"),
    ("chr2", 179397614, "A", "G", "TTN-AS1", 59.7, "PASS"),
    ("chr17", 41244725, "A", "G", "BRCA1", 95.5, "PASS"),
    ("chr17", 41244728, "A", "G", "BRCA1", 56.6, "LowQual"),
    ("chr3", 121264707, "C", "G", "POLQ", 91.9, "PASS"),
    ("chr2", 179397745, "C", "G", "TTN-AS1", 82.5, "LowQual"),
    ("chr3", 121303788, "G", "A", "ARGFX", 64.5, "PASS"),
    ("chr2", 179397763, "T", "G", "TTN-AS1", 80.4, "PASS"),
    ("chr17", 41244749, "A", "G", "BRCA1", 63.4, "PASS"),
    ("chr2", 179397799, "T", "A", "TTN-AS1", 97.4, "LowQual"),
    ("chr17", 41244750, "C", "T", "BRCA1", 64.3, "LowQual"),
    ("chr2", 179397889, "C", "A", "TTN-AS1", 57.2, "PASS"),
    ("chr17", 41244764, "G", "A", "BRCA1", 58.2, "PASS"),
    ("chr2", 179398106, "G", "A", "TTN-AS1", 51.4, "PASS"),
    ("chr2", 179398402, "C", "A", "TTN-AS1", 64.3, "PASS"),
    ("chr2", 179398532, "A", "G", "TTN-AS1", 61.9, "PASS"),
    ("chr2", 179398542, "T", "A", "TTN-AS1", 77.2, "PASS"),
    ("chr2", 179398643, "A", "G", "TTN-AS1", 78.0, "PASS"),
    ("chr2", 179398747, "T", "C", "TTN-AS1", 68.6, "PASS"),
    ("chr2", 179398751, "T", "G", "TTN-AS1", 60.4, "PASS"),
    ("chr2", 179398756, "C", "T", "TTN-AS1", 94.1, "LowQual"),
    ("chr17", 41244855, "T", "G", "BRCA1", 91.0, "PASS"),
    ("chr17", 41244859, "G", "A", "BRCA1", 61.9, "LowQual"),
    ("chr2", 179398896, "T", "G", "TTN-AS1", 73.9, "LowQual"),
    ("chr2", 179398897, "C", "T", "TTN-AS1", 85.0, "PASS"),
    ("chr2", 179398971, "C", "T", "TTN-AS1", 92.8, "LowQual"),
    ("chr2", 179399030, "C", "T", "TTN-AS1", 61.2, "LowQual"),
    ("chr17", 41244877, "A", "C", "BRCA1", 53.9, "PASS"),
    ("chr2", 179399227, "A", "G", "TTN-AS1", 96.8, "PASS"),
    ("chr17", 41244898, "T", "C", "BRCA1", 64.6, "PASS"),
    ("chr2", 179399301, "G", "T", "TTN-AS1", 55.4, "PASS"),
    ("chr2", 179399302, "G", "T", "TTN-AS1", 81.6, "PASS"),
    ("chr2", 179399356, "T", "C", "TTN-AS1", 90.4, "PASS"),
    ("chr2", 179399411, "A", "C", "TTN-AS1", 65.2, "PASS"),
    ("chr2", 39278351, "T", "G", "SOS1", 74.1, "PASS"),
    ("chr2", 47748266, "T", "G", "LOC129933697", 61.8, "LowQual"),
    ("chr2", 47748270, "T", "G", "LOC129933697", 82.2, "PASS"),
    ("chr2", 47748388, "G", "A", "MSH2", 61.9, "LowQual"),
    ("chr2", 236653414, "C", "T", "AGAP1", 81.4, "LowQual"),
    ("chr2", 39278371, "G", "A", "SOS1", 90.1, "LowQual"),
    ("chr2", 39278396, "A", "G", "SOS1", 67.1, "LowQual"),
    ("chr2", 39278406, "C", "A", "SOS1", 76.6, "PASS"),
    ("chr2", 39281754, "C", "T", "SOS1", 55.7, "PASS"),
    ("chr3", 123337556, "A", "G", "MYLK-AS1", 90.6, "PASS"),
    ("chr2", 48010360, "G", "A", "MSH6", 68.6, "PASS"),
    ("chr2", 39281833, "T", "A", "SOS1", 78.8, "PASS"),
    ("chr2", 39281854, "T", "C", "SOS1", 94.3, "PASS"),
    ("chr2", 236877126, "G", "T", "AGAP1", 50.3, "PASS"),
    ("chr2", 39281905, "G", "A", "SOS1", 93.1, "LowQual"),
    ("chr2", 236949492, "G", "A", "AGAP1", 90.9, "PASS"),
    ("chr2", 48026133, "G", "A", "MSH6", 85.0, "PASS"),
    ("chr3", 124456447, "C", "T", "UMPS", 80.5, "PASS"),
    ("chr2", 48026137, "G", "C", "MSH6", 88.9, "PASS"),
    ("chr3", 127786822, "G", "A", "RUVBL1", 90.6, "PASS"),
    ("chr2", 211504788, "A", "G", "CPS1", 62.9, "PASS"),
    ("chr2", 44059096, "T", "C", "ABCG5", 88.6, "PASS"),
    ("chr2", 238283255, "G", "A", "COL6A3", 52.3, "PASS"),
    ("chr2", 238283259, "C", "G", "COL6A3", 61.9, "PASS"),
    ("chr3", 127788349, "G", "C", "RUVBL1", 91.6, "PASS"),
    ("chr3", 124456915, "G", "C", "UMPS", 93.5, "PASS"),
    ("chr2", 48026161, "G", "A", "MSH6", 94.6, "PASS"),
    ("chr3", 124456962, "T", "A", "UMPS", 93.0, "PASS"),
    ("chr2", 44059149, "C", "T", "ABCG5", 99.1, "PASS"),
    ("chr2", 238283311, "G", "A", "COL6A3", 88.6, "PASS"),
    ("chr2", 44059163, "A", "G", "ABCG5", 87.9, "LowQual"),
    ("chr3", 124459035, "A", "G", "UMPS", 61.7, "PASS"),
    ("chr3", 124460980, "C", "T", "UMPS", 92.5, "LowQual"),
    ("chr2", 238283404, "G", "A", "COL6A3", 90.8, "LowQual"),
    ("chr17", 41245738, "T", "C", "BRCA1", 87.1, "LowQual"),
    ("chr2", 238283453, "G", "A", "COL6A3", 63.2, "PASS"),
    ("chr2", 211512682, "C", "T", "CPS1", 51.3, "PASS"),
    ("chr2", 211512700, "G", "A", "CPS1", 54.8, "PASS"),
    ("chr2", 238283515, "G", "A", "COL6A3", 85.8, "PASS"),
    ("chr2", 238283563, "G", "T", "COL6A3", 80.2, "LowQual"),
    ("chr2", 238283596, "C", "A", "COL6A3", 86.2, "PASS"),
    ("chr2", 44065001, "C", "T", "ABCG5", 75.3, "PASS"),
    ("chr2", 44065026, "T", "C", "ABCG5", 62.8, "PASS"),
    ("chr3", 12785464, "G", "C", "TMEM40", 61.0, "PASS"),
    ("chr2", 48026194, "G", "C", "MSH6", 53.6, "PASS"),
    ("chr2", 238285406, "C", "G", "COL6A3", 81.0, "LowQual"),
    ("chr2", 48026200, "A", "C", "MSH6", 57.3, "LowQual"),
    ("chr2", 44073312, "G", "A", "ABCG8", 83.8, "LowQual"),
    ("chr2", 211523352, "G", "A", "CPS1", 85.1, "PASS"),
    ("chr2", 211523357, "T", "A", "CPS1", 66.3, "LowQual"),
    ("chr2", 211523370, "T", "C", "CPS1", 60.0, "PASS"),
    ("chr3", 128199875, "G", "A", "GATA2", 88.6, "PASS"),
    ("chr2", 211523426, "A", "G", "CPS1", 76.6, "PASS"),
    ("chr2", 211523457, "C", "T", "CPS1", 74.5, "PASS"),
    ("chr2", 238287375, "C", "T", "COL6A3", 70.8, "PASS"),
    ("chr2", 238287379, "C", "T", "COL6A3", 54.4, "PASS"),
    ("chr3", 128199901, "G", "A", "GATA2", 86.7, "PASS"),
    ("chr2", 44078713, "G", "A", "ABCG8", 90.3, "PASS"),
    ("chr2", 48026307, "A", "G", "MSH6", 64.1, "PASS"),
    ("chr2", 238287460, "C", "T", "COL6A3", 70.1, "LowQual"),
    ("chr3", 124567364, "C", "T", "ITGB5", 88.7, "PASS"),
    ("chr2", 211525295, "G", "A", "CPS1", 51.7, "PASS"),
    ("chr3", 12457922, "C", "T", "PPARG", 84.3, "PASS"),
    ("chr2", 238287492, "C", "T", "COL6A3", 59.5, "PASS"),
    ("chr2", 44078779, "A", "G", "ABCG8", 51.7, "PASS"),
    ("chr3", 12458274, "C", "T", "PPARG", 55.6, "PASS"),
    ("chr3", 128199936, "T", "A", "GATA2", 78.1, "PASS"),
    ("chr2", 211525361, "T", "G", "CPS1", 52.1, "PASS"),
    ("chr2", 44079544, "G", "A", "ABCG8", 71.9, "PASS"),
    ("chr17", 41245871, "A", "C", "BRCA1", 64.1, "PASS"),
    ("chr2", 238287856, "G", "T", "COL6A3", 76.3, "PASS"),
    ("chr2", 44079574, "G", "A", "ABCG8", 54.2, "PASS"),
    ("chr2", 48026379, "G", "A", "MSH6", 58.6, "LowQual"),
    ("chr3", 128200044, "T", "C", "GATA2", 75.9, "PASS"),
    ("chr2", 44079623, "C", "A", "ABCG8", 68.4, "PASS"),
    ("chr3", 124738121, "G", "A", "HEG1", 85.9, "PASS"),
    ("chr3", 124738355, "C", "T", "HEG1", 93.8, "PASS"),
    ("chr2", 48026399, "G", "A", "MSH6", 51.2, "PASS"),
    ("chr2", 44079773, "G", "T", "ABCG8", 54.7, "LowQual"),
    ("chr2", 44079785, "G", "A", "ABCG8", 57.4, "PASS"),
    ("chr3", 128200089, "T", "G", "GATA2", 80.7, "PASS"),
    ("chr2", 211540496, "T", "C", "CPS1", 73.8, "PASS"),
    ("chr2", 211540514, "G", "C", "CPS1", 67.5, "PASS"),
    ("chr2", 238289779, "C", "T", "COL6A3", 83.3, "PASS"),
    ("chr3", 124952066, "G", "A", "ZNF148", 80.5, "LowQual"),
    ("chr2", 48026491, "G", "T", "MSH6", 75.5, "PASS"),
    ("chr3", 128200724, "G", "C", "GATA2", 83.7, "LowQual"),
    ("chr2", 44100983, "G", "T", "ABCG8", 65.6, "PASS"),
    ("chr2", 212248389, "C", "T", "ERBB4", 93.3, "LowQual"),
    ("chr3", 124953141, "T", "A", "ZNF148", 61.6, "LowQual"),
    ("chr17", 41245952, "T", "A", "BRCA1", 87.1, "PASS"),
    ("chr2", 238296516, "G", "A", "COL6A3", 78.5, "PASS"),
    ("chr3", 128200744, "G", "C", "GATA2", 54.8, "LowQual"),
    ("chr2", 48026507, "C", "G", "MSH6", 93.0, "LowQual"),
    ("chr2", 238296572, "A", "T", "COL6A3", 83.1, "PASS"),
    ("chr2", 44101126, "G", "T", "ABCG8", 83.4, "PASS"),
    ("chr2", 238296587, "C", "T", "COL6A3", 55.0, "PASS"),
    ("chr3", 125179681, "A", "C", "SNX4", 91.7, "PASS"),
    ("chr2", 238296624, "C", "A", "COL6A3", 84.9, "PASS"),
    ("chr2", 21224895, "C", "T", "APOB", 79.8, "PASS"),
    ("chr3", 128200770, "G", "A", "GATA2", 71.6, "LowQual"),
    ("chr2", 21224917, "A", "G", "APOB", 74.4, "PASS"),
    ("chr2", 21224962, "C", "G", "APOB", 74.6, "PASS"),
    ("chr2", 238296716, "A", "G", "COL6A3", 95.4, "LowQual"),
    ("chr2", 238296718, "T", "C", "COL6A3", 92.9, "PASS"),
    ("chr17", 41245974, "A", "G", "BRCA1", 98.7, "PASS"),
    ("chr2", 44102301, "C", "T", "ABCG8", 64.7, "PASS"),
    ("chr2", 21225103, "T", "C", "APOB", 53.9, "PASS"),
    ("chr2", 48026550, "G", "A", "MSH6", 81.7, "PASS"),
    ("chr2", 238303218, "C", "T", "COL6A3", 67.9, "LowQual"),
    ("chr3", 125279351, "T", "C", "OSBPL11", 77.2, "PASS"),
    ("chr3", 125282600, "C", "A", "OSBPL11", 61.6, "PASS"),
    ("chr3", 14220139, "G", "A", "XPC", 82.3, "PASS"),
    ("chr3", 142203986, "C", "T", "ATR", 86.9, "PASS"),
    ("chr3", 142204005, "C", "G", "ATR", 90.6, "LowQual"),
    ("chr3", 142204006, "C", "T", "ATR", 87.3, "PASS"),
    ("chr3", 142204095, "C", "T", "ATR", 61.4, "PASS"),
    ("chr3", 142204102, "T", "G", "ATR", 68.7, "PASS"),
    ("chr3", 142212079, "A", "G", "ATR", 63.1, "LowQual"),
    ("chr3", 142212097, "A", "G", "ATR", 66.1, "PASS"),
    ("chr3", 142215121, "T", "A", "ATR", 61.1, "LowQual"),
    ("chr3", 142215143, "T", "C", "ATR", 89.4, "PASS"),
    ("chr3", 142215249, "C", "G", "ATR", 66.9, "PASS"),
    ("chr3", 142215318, "G", "A", "ATR", 56.2, "PASS"),
    ("chr3", 142215872, "T", "C", "ATR", 69.4, "PASS"),
    ("chr3", 142215882, "C", "T", "ATR", 88.1, "LowQual"),
    ("chr3", 142215912, "T", "C", "ATR", 89.1, "LowQual"),
    ("chr3", 142215975, "C", "T", "ATR", 98.5, "PASS"),
    ("chr3", 142216034, "T", "A", "ATR", 84.7, "LowQual"),
    ("chr3", 142217354, "A", "G", "ATR", 57.1, "LowQual"),
    ("chr3", 142217570, "T", "C", "ATR", 78.6, "PASS"),
    ("chr3", 142217595, "C", "T", "ATR", 58.7, "PASS"),
    ("chr3", 142218533, "C", "T", "ATR", 70.2, "LowQual"),
    ("chr3", 142222234, "A", "G", "ATR", 90.0, "PASS"),
    ("chr3", 142222281, "A", "G", "ATR", 85.0, "PASS"),
    ("chr3", 142223967, "A", "G", "ATR", 60.8, "PASS"),
    ("chr3", 142223980, "C", "T", "ATR", 53.8, "PASS"),
    ("chr3", 142224008, "G", "A", "ATR", 66.8, "PASS"),
    ("chr3", 142224097, "C", "T", "ATR", 50.8, "LowQual"),
    ("chr3", 142226783, "C", "T", "ATR", 70.3, "PASS"),
    ("chr3", 142226797, "A", "C", "ATR", 93.9, "LowQual"),
    ("chr3", 142226816, "G", "A", "ATR", 82.1, "LowQual"),
    ("chr3", 142231248, "A", "T", "ATR", 92.0, "LowQual"),
    ("chr3", 142231262, "T", "C", "ATR", 93.4, "PASS"),
    ("chr3", 142231292, "T", "C", "ATR", 74.4, "LowQual"),
    ("chr3", 142232428, "T", "C", "ATR", 91.4, "PASS"),
    ("chr3", 142234273, "T", "C", "ATR", 87.7, "PASS"),
    ("chr3", 142234312, "C", "G", "ATR", 90.7, "LowQual"),
    ("chr3", 142234374, "T", "G", "ATR", 88.3, "LowQual"),
    ("chr3", 142238540, "C", "T", "ATR", 78.8, "LowQual"),
    ("chr3", 142238545, "C", "T", "ATR", 89.3, "PASS"),
    ("chr3", 142238570, "T", "A", "ATR", 91.7, "PASS"),
    ("chr3", 142241561, "C", "A", "ATR", 83.7, "PASS"),
    ("chr2", 23865607, "G", "C", "KLHL29", 50.1, "PASS"),
    ("chr2", 238657952, "C", "T", "LRRFIP1", 86.2, "PASS"),
    ("chr3", 128204688, "G", "A", "GATA2", 57.8, "PASS"),
    ("chr2", 48026752, "G", "A", "MSH6", 68.6, "PASS"),
    ("chr17", 41246130, "T", "A", "BRCA1", 72.7, "PASS"),
    ("chr2", 44126446, "T", "C", "LRPPRC", 82.4, "PASS"),
    ("chr2", 44126448, "G", "A", "LRPPRC", 94.9, "PASS"),
    ("chr2", 238671987, "C", "G", "LRRFIP1", 69.2, "PASS"),
    ("chr3", 125877266, "C", "T", "ALDH1L1", 84.5, "PASS"),
    ("chr2", 44126604, "C", "A", "LRPPRC", 70.9, "PASS"),
    ("chr2", 44126633, "C", "T", "LRPPRC", 53.4, "PASS"),
    ("chr3", 126070801, "T", "C", "KLF15", 59.4, "PASS"),
    ("chr2", 212285103, "T", "C", "ERBB4", 89.4, "PASS"),
    ("chr2", 238726028, "G", "A", "RBM44", 89.3, "PASS"),
    ("chr2", 212285146, "T", "G", "ERBB4", 51.3, "PASS"),
    ("chr2", 238726261, "A", "C", "RBM44", 68.7, "PASS"),
    ("chr2", 238726976, "A", "C", "RBM44", 61.6, "PASS"),
    ("chr3", 128204763, "G", "A", "GATA2", 89.7, "LowQual"),
    ("chr3", 128204766, "A", "G", "GATA2", 66.8, "PASS"),
    ("chr2", 21228559, "A", "G", "APOB", 94.2, "PASS"),
    ("chr2", 48026797, "T", "C", "MSH6", 58.3, "PASS"),
    ("chr2", 238728918, "G", "A", "RBM44", 98.8, "PASS"),
    ("chr2", 238729784, "G", "T", "RBM44", 53.9, "PASS"),
    ("chr3", 12611651, "C", "G", "MKRN2", 93.8, "PASS"),
    ("chr3", 126135309, "G", "T", "CFAP100", 83.2, "PASS"),
    ("chr3", 128204802, "G", "A", "GATA2", 75.8, "LowQual"),
    ("chr3", 142280091, "G", "A", "ATR", 95.6, "LowQual"),
    ("chr3", 142280121, "A", "G", "ATR", 55.1, "PASS"),
    ("chr3", 142280179, "T", "C", "ATR", 76.3, "PASS"),
    ("chr3", 142281098, "C", "T", "ATR", 93.7, "PASS"),
    ("chr3", 142281117, "C", "T", "ATR", 89.2, "PASS"),
    ("chr3", 142281190, "A", "G", "ATR", 58.2, "PASS"),
    ("chr3", 142281311, "T", "G", "ATR", 67.9, "PASS"),
    ("chr3", 142281367, "C", "T", "ATR", 59.5, "PASS"),
    ("chr3", 142281406, "G", "A", "ATR", 87.1, "PASS"),
    ("chr3", 142281465, "C", "T", "ATR", 87.5, "PASS"),
    ("chr3", 142281495, "C", "G", "ATR", 71.4, "PASS"),
    ("chr3", 142281519, "G", "T", "ATR", 82.4, "PASS"),
    ("chr3", 142281533, "T", "G", "ATR", 58.9, "PASS"),
    ("chr3", 142281602, "A", "G", "ATR", 81.6, "PASS"),
    ("chr3", 142281658, "A", "G", "ATR", 64.3, "PASS"),
    ("chr3", 142281683, "T", "C", "ATR", 94.2, "PASS"),
    ("chr3", 142281715, "G", "C", "ATR", 83.1, "LowQual"),
    ("chr3", 142281741, "G", "C", "ATR", 63.3, "PASS"),
    ("chr3", 142281755, "A", "T", "ATR", 66.1, "PASS"),
    ("chr3", 142281797, "T", "C", "ATR", 97.0, "PASS"),
    ("chr3", 142281858, "G", "A", "ATR", 59.1, "PASS"),
    ("chr3", 128204888, "G", "T", "GATA2", 57.5, "PASS"),
    ("chr2", 48026856, "T", "C", "MSH6", 83.8, "PASS"),
    ("chr3", 128204897, "A", "G", "GATA2", 72.3, "LowQual"),
    ("chr17", 41246176, "C", "T", "BRCA1", 55.2, "PASS"),
    ("chr2", 44139636, "G", "A", "LRPPRC", 75.6, "LowQual"),
    ("chr2", 239009215, "T", "G", "ESPNL", 55.6, "PASS"),
    ("chr3", 128204905, "T", "G", "GATA2", 89.7, "PASS"),
    ("chr2", 44139696, "C", "T", "LRPPRC", 77.7, "LowQual"),
    ("chr2", 21229033, "G", "A", "APOB", 68.6, "PASS"),
    ("chr2", 44145150, "C", "G", "LRPPRC", 54.9, "PASS"),
    ("chr2", 21229088, "G", "C", "APOB", 94.0, "PASS"),
    ("chr2", 44145219, "T", "G", "LRPPRC", 71.5, "LowQual"),
    ("chr2", 21229159, "C", "T", "APOB", 74.4, "PASS"),
]


MYVARIANT_URL = "https://myvariant.info/v1/query"
MYVARIANT_FIELDS = "chrom,vcf.position,vcf.ref,vcf.alt,clinvar.gene.symbol"
MYVARIANT_TIMEOUT = 12

QUERY_PATHOGENIC = "clinvar.rcv.clinical_significance:Pathogenic AND _exists_:vcf"
QUERY_OTHER = (
    "(clinvar.rcv.clinical_significance:Benign"
    " OR clinvar.rcv.clinical_significance:\"Likely benign\""
    " OR clinvar.rcv.clinical_significance:\"Uncertain significance\")"
    " AND _exists_:vcf"
)


def _myvariant_query(q: str, size: int, offset: int) -> list[tuple]:
    url = (
        f"{MYVARIANT_URL}"
        f"?q={quote(q)}"
        f"&fields={MYVARIANT_FIELDS}"
        f"&size={size}"
        f"&from={offset}"
        f"&assembly=hg38"
    )
    with urlopen(url, timeout=MYVARIANT_TIMEOUT) as resp:
        data = json.loads(resp.read())

    results = []
    for hit in data.get("hits", []):
        vcf = hit.get("vcf") or {}
        pos = vcf.get("position")
        ref = vcf.get("ref")
        alt = vcf.get("alt")
        gene = (hit.get("clinvar") or {}).get("gene", {}).get("symbol")
        chrom = hit.get("chrom")
        if not all([pos, ref, alt, gene, chrom]):
            continue
        if len(ref) > 10 or len(alt) > 10:
            continue
        results.append((f"chr{chrom}", int(pos), ref, alt, gene))
    return results


def fetch_live_variants(rng: random.Random, n_total: int = 30, n_pathogenic: int = 2) -> list[tuple]:
    variants: list[tuple] = []

    path_offset = rng.randint(0, 5000)
    try:
        raw = _myvariant_query(QUERY_PATHOGENIC, n_pathogenic * 4, path_offset)
        sampled = rng.sample(raw, min(n_pathogenic, len(raw)))
        variants.extend(sampled)
        print(f"[MOCK] myvariant.info: fetched {len(sampled)} pathogenic variants (offset={path_offset})")
    except Exception as exc:
        print(f"[MOCK] myvariant.info pathogenic fetch failed: {exc}")

    n_remaining = n_total - len(variants)
    if n_remaining > 0:
        other_offset = rng.randint(0, 5000)
        try:
            raw = _myvariant_query(QUERY_OTHER, n_remaining * 3, other_offset)
            sampled = rng.sample(raw, min(n_remaining, len(raw)))
            variants.extend(sampled)
            print(f"[MOCK] myvariant.info: fetched {len(sampled)} other variants (offset={other_offset})")
        except Exception as exc:
            print(f"[MOCK] myvariant.info other fetch failed: {exc}")

    for i, v in enumerate(variants):
        qual = round(rng.uniform(50.0, 99.9), 1)
        filt = rng.choices(["PASS", "LowQual"], weights=[3, 1])[0]
        variants[i] = (*v, qual, filt)

    return variants


VCF_HEADER_FQ2BAM = """##fileformat=VCFv4.2
##source=MockParabricks-HaplotypeCaller
##reference=hg38
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##FILTER=<ID=LowQual,Description="Low quality variant">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE"""

VCF_HEADER_DEEPVARIANT = """##fileformat=VCFv4.2
##source=MockParabricks-DeepVariant
##reference=hg38
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=DVQ,Number=1,Type=Float,Description="DeepVariant Quality">
##FILTER=<ID=LowQual,Description="Low quality variant">
##FILTER=<ID=RefCall,Description="Reference call by DeepVariant">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE"""


def generate_vcf(patient_id: str, sample_id: str, num_variants: int = 50, deepvariant: bool = False) -> str:
    random.seed(sample_id)
    rng = random.Random(sample_id)

    N_LIVE      = 30
    N_STATIC    = 20
    N_PATHOGENIC_LIVE   = 2
    N_PATHOGENIC_STATIC = random.randint(1, 2)

    live = fetch_live_variants(rng, n_total=N_LIVE, n_pathogenic=N_PATHOGENIC_LIVE)
    live_count = len(live)
    print(f"[MOCK] myvariant.info returned {live_count} live variants")

    n_static_needed = (50 - live_count)
    n_path_static   = min(N_PATHOGENIC_STATIC, len(PATHOGENIC_VARIANTS))
    n_other_static  = max(0, n_static_needed - n_path_static)

    static_pathogenic = random.sample(PATHOGENIC_VARIANTS, n_path_static)
    static_other      = random.sample(OTHER_VARIANTS, min(n_other_static, len(OTHER_VARIANTS)))
    static_variants   = static_pathogenic + static_other

    selected = live + static_variants
    selected.sort(key=lambda v: (v[0], v[1]))

    header = VCF_HEADER_DEEPVARIANT if deepvariant else VCF_HEADER_FQ2BAM
    lines = [header]

    for chrom, pos, ref, alt, gene, qual, filt in selected:
        depth = random.randint(30, 200)
        af = round(random.uniform(0.1, 0.9), 3)
        gt = random.choice(["0/1", "1/1"])

        if deepvariant:
            dvq = round(qual + random.uniform(-5, 10), 1)
            info = f"DP={depth};AF={af};DVQ={dvq}"
            gq = random.randint(20, 99)
            lines.append(f"{chrom}	{pos}	.	{ref}	{alt}	{qual:.1f}	{filt}	{info}	GT:DP:GQ	{gt}:{depth}:{gq}")
        else:
            info = f"DP={depth};AF={af}"
            lines.append(f"{chrom}	{pos}	.	{ref}	{alt}	{qual:.1f}	{filt}	{info}	GT:DP	{gt}:{depth}")
    
    random.seed()
    
    return "\n".join(lines) + "\n"


def run_fq2bam(args):
    print(f"[MOCK] Parabricks fq2bam starting")
    print(f"[MOCK] Input FASTQ: {args.in_fq}")
    print(f"[MOCK] Reference: {args.ref}")
    print(f"[MOCK] Output BAM: {args.out_bam}")

    stages = [
        ("Loading reference genome", 10),
        ("Aligning reads (BWA-MEM2)", 20),
        ("Sorting alignments", 5),
        ("Marking duplicates", 5),
        ("Base quality recalibration", 10),
        ("Writing BAM", 5),
    ]

    for stage_name, duration in stages:
        print(f"[MOCK] {stage_name}...")
        time.sleep(duration)

    bam_path = Path(args.out_bam)
    bam_path.parent.mkdir(parents=True, exist_ok=True)
    bam_path.write_text("MOCK_BAM_FILE\n")

    print(f"[MOCK] BAM written to: {bam_path}")
    print(f"[MOCK] Parabricks fq2bam complete")


def run_deepvariant(args):
    print(f"[MOCK] Parabricks DeepVariant starting")
    print(f"[MOCK] Input BAM: {args.in_bam}")
    print(f"[MOCK] Output VCF: {args.out_variants}")

    stages = [
        ("Loading model weights", 10),
        ("Making pileup examples", 15),
        ("Calling variants (DeepVariant CNN)", 20),
        ("Genotyping variants", 10),
        ("Writing VCF", 5),
    ]

    for stage_name, duration in stages:
        print(f"[MOCK] {stage_name}...")
        time.sleep(duration)

    vcf_path = Path(args.out_variants)
    vcf_path.parent.mkdir(parents=True, exist_ok=True)

    sample_id = vcf_path.stem
    patient_id = vcf_path.parent.parent.name
    
    vcf_content = generate_vcf(patient_id, sample_id, args.num_variants, deepvariant=True)
    vcf_path.write_text(vcf_content)

    variant_count = sum(1 for line in vcf_content.splitlines() if not line.startswith("#"))
    print(f"[MOCK] DeepVariant called {variant_count} variants")
    print(f"[MOCK] VCF written to: {vcf_path}")
    print(f"[MOCK] Parabricks DeepVariant complete")


def run_deepvariant_germline(args):
    print(f"[MOCK] Parabricks DeepVariant Germline starting")
    print(f"[MOCK] Output VCF: {args.out_variants}")

    stages = [
        ("Loading model weights", 2),
        ("Aligning and Making pileup examples", 3),
        ("Calling variants (DeepVariant CNN)", 4),
        ("Writing VCF", 1),
    ]

    for stage_name, duration in stages:
        print(f"[MOCK] {stage_name}...")
        time.sleep(duration)

    vcf_path = Path(args.out_variants)
    vcf_path.parent.mkdir(parents=True, exist_ok=True)

    sample_id = vcf_path.stem
    patient_id = vcf_path.parent.parent.name
    
    vcf_content = generate_vcf(patient_id, sample_id, args.num_variants, deepvariant=True)
    vcf_path.write_text(vcf_content)

    variant_count = sum(1 for line in vcf_content.splitlines() if not line.startswith("#"))
    print(f"[MOCK] DeepVariant called {variant_count} variants")
    print(f"[MOCK] VCF written to: {vcf_path}")
    print(f"[MOCK] Parabricks DeepVariant Germline complete")

def main():
    parser = argparse.ArgumentParser(description="Mock Parabricks pbrun")
    subparsers = parser.add_subparsers(dest="command")

    fq2bam = subparsers.add_parser("fq2bam")
    fq2bam.add_argument("--ref", default="/data/refs/hg38.fa")
    fq2bam.add_argument("--in-fq", required=True)
    fq2bam.add_argument("--out-bam", required=True)
    fq2bam.add_argument("--num-variants", type=int, default=8)

    dv = subparsers.add_parser("deepvariant")
    dv.add_argument("--ref", default="/data/refs/hg38.fa")
    dv.add_argument("--in-bam", required=True)
    dv.add_argument("--out-variants", required=True)
    dv.add_argument("--num-variants", type=int, default=8)

    dvg = subparsers.add_parser("deepvariant_germline")
    dvg.add_argument("--out-variants", required=True)
    dvg.add_argument("--num-variants", type=int, default=8)

    args, unknown = parser.parse_known_args()

    if args.command == "fq2bam":
        run_fq2bam(args)
    elif args.command == "deepvariant":
        run_deepvariant(args)
    elif args.command == "deepvariant_germline":
        run_deepvariant_germline(args)
    else:
        parser.print_help()


if __name__ == "__main__":
    main()