I have two strains, X and Y, and I would like to compare the variants found in both. I have my own parent strain, Z, that was sequenced and assembled to be used as the reference genome.
I first aligned X and Y to Z using minimap2 and then I used FreeBayes as the variant caller. Once I had the two separate VCF files I looked online to see what was the best way to filter out the unique and common variants in X and Y.
I found the
bcftools isec tool to be my best bet so I went ahead and ran this line of code:
./bcftools isec -p out/path/ X.vcf.gz Y.vcf.gz
Now I have three new VCF files:
0000.vcf(variants unique to X)
0001.vcf(variants unique to Y)
0002.vcf(variants in both X and Y)
However, it's still in VCF format. I need a way to parse through the VCF file to list out the SNPs with high quality with their position on the genome. I tried using
bcftools stats but it just lists out how many SNPs there are and not their position.
TLDR: Can someone help me find a way to list out the locations of SNPs from a VCF file in human readable format?