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I'm attempting to use Variant Annotator to annotate some VCFs produced by samtools so I can run VQSR on them. Unfortunately I've gottent stuck and I'm trying to figure out why Variant Annotator wouldn't be annotating INDELs with MappingQualityRankSumTest and ReadPosRankSumTest, it seems to annotate SNPs fine. There are both Homs and het's called on the sample. Could it be I need to left align the indels to get enough coverage? What would you suggest is the best way to debug this? Is there a way to make GATK behave more verbosely about why it's refusing an annotation?
Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute