This is s simple repository for mapping reads, SNP calling and other SNP-related operations
a simple script that extracts all the SNPS from a set of VCF files and creates a two-column table
column 1 is the base coordinate and column 2 is the total number of SNPs for that base in the set of VCF files
just run it in a folder with the VCF files and provide the gene number:
e. g. perl SNP_PLOTTER.pl g999
outputs are 4 files, each has a table, all snps, and codons 1,2 and 3
how to use: sh map_and_vcf.sh #usage: $1= read suffix $2= reference.fasta the .fna file is the reference genome/gene set in fasta file in this case REF is an alias for the index
A simple script to count the SNPS per gene input: one or more vcf files obtained wit the map_and_vcf.sh script output a table use: place this script in the same directory as the vcf files that you want to iclude in the table and run find the total number of genes in the reference genome (e. g. grep ">" reference.fna -c) perl RAW_SNP_counter.pl 8722
by Pablo pcruzm@biosustain.dt.dk
10-1-23,