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Old 01-23-2014, 06:24 AM   #1
milesgr
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Location: NJ

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Default GATK variant calling statistics...

Hi all,
We are calling variants on partial exome data using GATK. We want to see what fraction of our samples have a particular variant. As constituted, GATK will give us the set of samples containing the particular variant. Any sample that doesn't will simply exclude it from the VCF. My question is whether or not there is a way to distinguish the samples that have a true wild-type phenotype (and thus no variant call) from those that aren't called due to poor quality score (and thus should be excluded from our percentages since the phenotype cannot be determined). Thank you very much in advance for your help.
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Old 01-23-2014, 10:01 AM   #2
vdauwera
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Default

There are two ways to deal with this. One is to use the EMIT_ALL_SITES option of UnifiedGenotyper and enable calculation of reference PLs. The other, which is better, is to call variants with HalpotypeCaller (GATK's newer variant caller) and use the -ERC option to generate a gVCF.

For more details, see the online GATK documentation and please post any follow-up questions on the GATK support forum.

http://www.broadinstitute.org/gatk/guide/
http://gatkforums.broadinstitute.org/
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