Calling Snps From Libraries

Question

[yevishere]

I have been struggling with something that should be easy. There are many software packages for calling SNPs but I am having trouble to get them what I want. I want to compare my Illumina sequencing results to the previously genotyped SNP calls for the sake of quality control. Basically given a list of SNPs and positions, I want to be able to find out what the "call" is from multiple libraries regardless of coverage. For example given this kind of file:

snp chr pos

rs1 chr1 100

rs2 chr2 300

rs3 chr2 1000

I want this kind of file:

snp chr pos library1 coverage1 Library2 coverage2

rs1 chr1 100 A 10 A 20

rs2 chr2 300 C 1 C 10

rs3 chr2 1000 C 2 G 100

Thanks!

Answer 1

[User 59]

You want vcftools

Check out vcf-isec to do the comparisons.