Dear GATK developers,
It is easy to understand the annotations such as FS, SOR, ReadPosRankSum for a specific sample. However, how is the value calculated for a jointly called genotype file? I guess they are aggregated from individual annotations from individual samples. Could you provide the detail on the aggregation? Is it a simple average of all annotations from each sample?
Here is an example. For a specific site, if we have 100 ReadPosRankSum values from each gvcf file. In the jointly called genotype file, ther is only one single value of ReadPosRankSum for this site. How is this single value calculated from the 100 raw values? If for different annotation values, there are different ways, could you please explain how they are aggregated for the following: MQRankSum, ReadPosRankSum, InbreedingCoeff, FS, SOR, MQ, QD?
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