SNP calling from pool sequencing with freebayes

Question

[marcoabbestia]

Hi all

I have NGS data from 5 pools of 5 different breeds. My idea is to find a set of SNPs that identify each breed, then a SNP that is present only in one breed and not in the other four. I used several software and filters but when I visualize the results with IGV or Genome Browser the same SNP is present in more than one breed although with a lower number of reads supporting that SNP. Please could you help me to set the filters with Freebayes? any suggestions will be very appreciated.

greetings

Marco

Answer 1

[h.mon]

Have you tried the suggestions on How To Efficiently Remove Snps That Are Present In All Samples? thread?

[marcoabbestia]

Thank you, I saw the suggestions But I think that my problem is a little different. In that suggestion he wants to remove the SNP that are common in all 32 samples, I'm interested to remove the SNPs that are present in at least 2 of my 5 samples, for example

A  B  C
1  2  1
2  3  3
5  5  5
7  8  9
99 99 99

where A, B and C are three different VCF files and I'd like to obtain 7, 8 e 9.

Any suggestion?