the "--heterozygosity" flag in GATK unifiedGenotyper

lre1234 · 10-01-2013, 06:15 AM

Hi all,
I am using the unifiedgenotyper and have a question about the "--heterozygosity" flag.

The default is "0.001". Does this mean that at a particular site, if this percentage of bases is the alternate allele, then the site will be called a het? Also, is this based on each individual sample, or the combined for all samples together.

Essentially, what I would like to do, is set a parameter in which a sample will be a het where at least 10% of the alleles are the alternate base, and to do this for each individual sample.

as an example. I got this set of genotypes:
GT:AD

P:GQ:PL 0/0:86,15:96:56:0,56,3283 0/1:36,36:72:99:1111,0,1293

These are at the same site. with ~17 of the sites being the alternate in the first sample, why is it being called as an "0/0".

It is possible I am just not understanding some of the principal points of everything (and there are probably multiple questions here).

Thanks for help...

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10-01-2013, 06:15 AM	#1
lre1234 Senior Member Location: US Join Date: Aug 2011 Posts: 106	the "--heterozygosity" flag in GATK unifiedGenotyper Hi all, I am using the unifiedgenotyper and have a question about the "--heterozygosity" flag. The default is "0.001". Does this mean that at a particular site, if this percentage of bases is the alternate allele, then the site will be called a het? Also, is this based on each individual sample, or the combined for all samples together. Essentially, what I would like to do, is set a parameter in which a sample will be a het where at least 10% of the alleles are the alternate base, and to do this for each individual sample. as an example. I got this set of genotypes: GT:ADP:GQ:PL 0/0:86,15:96:56:0,56,3283 0/1:36,36:72:99:1111,0,1293 These are at the same site. with ~17 of the sites being the alternate in the first sample, why is it being called as an "0/0". It is possible I am just not understanding some of the principal points of everything (and there are probably multiple questions here). Thanks for help...