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Old 04-07-2013, 03:55 PM   #5
Location: Las Vegas

Join Date: Mar 2012
Posts: 11

Calling species B and C against the reference together just saves space. And yes, you will still need to use the reference genome. The output is slightly different however, so what you will get is an extra GT field:
chr2	213263	.	A	C,T	72	.	DP=14;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,9,4;MQ=56;FQ=-60	GT:<Genotype of A>	GT:<Genotype of B>
I'm pretty sure that the PL field is reporting the quality score of all of the allelic possibilities, which is why you see six of them. You will have to consult the documentation for how to get multiple sample depth information.
Also, I find that the Broad Institute does a much better job documentation than does sourceforge or Since samtools and gatk both use VCF as the standard output, you might want to start with the GATK documentation if not just switch to GATK altogether.

Hope this helps.
Khen is offline   Reply With Quote