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Old 09-07-2011, 10:44 AM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

I'm not sure what you mean by "clearly", but you should see a 1/1, 0/1 or 0/0 in each entry. That tells you if the SNP is predicted to be homozygous alternate, heterozygous, or homozygous reference. Unfortunately, what you really want is the DP4 for each sample separately, and doing a multi-vcf with samtools won't do that. You'll need the individual vcf file to see that.
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