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Calling Snps From Libraries

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!

snp samtools bam snps
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updated by Biostar Biostar • written by yevishere • yevishere

1 answer

You want vcftools

Check out vcf-isec to do the comparisons.

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written by User 59 User 59

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