gatk HaplotyperCaller bam reference

Question

[Peter Chung]

I am new in WGS sequencing. I am working on the gatk HaplotypeCaller step. The bam file is required for calling variants.

I have generated a few bam files upstream starting from bwa. I have sample1.bam, sample1.addRG.bam for add read group and sample1.addRG.mkdup.bam for remove duplicates. Therefore, which one should I use for haplotypecaller step ?

Thank you for your advice.

Answer 1

[Pierre Lindenbaum]

sample1.addRG.mkdup.bam

see https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145