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Effect of using a ReduceReads bam or full bam on GATK 2.7 HaplotyeCaller+VQSR?
What is the expected effect of using GATK 2.7 HaplotyeCaller+VQSR on a WGS 30x bam or the same bam being processed through ReducedReads beforehand? Does one expect exactly the same variants called on both files or a small difference between them?
Do HaplotypeCaller or VQSR treat the input differently if it comes from a full WGS bam or a WGS reduced bam?