Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Effect of using a ReduceReads bam or full bam on GATK 2.7 HaplotyeCaller+VQSR?

avilellaavilella Posts: 6Member

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?

Best Answer

Answers

Sign In or Register to comment.