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I ran the same sample through a pipeline using GATK twice and received different variants. I am trying to understand the reason behind this. My samples are from a MiSeq/capture kit run and downsampling could be one reason (given in one scenario that variant is called and in other it isn't) the variant is called at 32% when looked into the .bam files.
As I understand the UnifiedGenotyper downsamples my dataset randomly to 250, so I played around with -dcov parameter
same sample run twice, 1st run reports a variant; 2nd run doesn't.
up -dcov to 1000 neither run reports the variant.
But setting -dt to NONE could be computationally exhaustive for a big sample set. Is there an identifiable reason to why this is happening..?