Datasets

1. Challenging medically relevant regions (CMRG) benchmark for HG002 sample (GRCh38) with high-confidence regions https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/GRCh38/SmallVariant/
2. GRCh38 original reference https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta.gz
3. GRCh38 modified reference: https://bcm.box.com/s/xi95ahgzrw86pvogm7sdwl0ppn49i5dn

HG002 HiFiasm assembly used for dipcall https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/hifiasm-assembly/

Dipcall (v0.3) https://github.com/lh3/dipcall
Minimap2 (v2.22 - r1101) https://github.com/lh3/minimap2/releases/tag/v2.22
Hap.py tool (v0.3.14) https://github.com/Illumina/hap.py

1000g samples https://github.com/human-pangenomics/hpgp-data

Whole Exome Sequencing (hiseq4000,wes_agilent,50x,HG002,grch38) https://storage.googleapis.com/brain-genomics-public/research/sequencing/grch38/bam/hiseq4000/wes_agilent/50x/HG002.hiseq4000.wes-agilent.50x.dedup.grch38.bam

WES high-confidence bed regions https://www.biorxiv.org/content/biorxiv/early/2020/12/16/2020.12.15.356360/DC2/embed/media-2.gz?download=true