gatk HaplotyperCaller bam reference
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5.9 years ago
Peter Chung ▴ 210

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.

gatk haplotypercaller bam • 2.1k views
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