gatk HaplotyperCaller bam reference
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.
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Peter Chung
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sample1.addRG.mkdup.bam
see https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145
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Pierre Lindenbaum
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