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dnanexus-archive / parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Apache License 2.0
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multiple bam files #57

Closed yyx8671 closed 5 years ago

yyx8671 commented 5 years ago

Hi,

I want to have a test using parliament2. I have multiple bam files for one sample. When I use parliament2, can I put each bam file by specifying a '--bam' option or I need to merge all bam files into one?

Thanks, Andy

slzarate commented 5 years ago

Hi Andy,

Parliament2 is only meant to be run on one WGS BAM file at a time. You can merge the BAM files into one, or run Parliament2 multiple times and merge the final VCF outputs (we already do that in Parliament2 using SURVIVOR).

yyx8671 commented 5 years ago

Thanks so much @slzarate for your reply.