Question: gatk HaplotyperCaller bam reference
0
gravatar for Peter Chung
19 months ago by
Peter Chung120
Hong Kong
Peter Chung120 wrote:

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.

bam gatk haplotypercaller • 634 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by Peter Chung120
1
gravatar for Pierre Lindenbaum
19 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:
sample1.addRG.mkdup.bam

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

workflow

ADD COMMENTlink modified 19 months ago • written 19 months ago by Pierre Lindenbaum129k
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