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.
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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