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Published 20 hours ago • verified publisher icon brentp

using duphold on a multisample trio VCF file

Open prasundutta87 opened this issue 1 year ago • 2 comments

Hi,

I have a multisample trio VCF file generated using Oxford Nanopore long read data. Is there any way where duphold can be used on a multisample VCF file?

Regards, Prasun

prasundutta87 avatar Sep 05 '22 17:09 prasundutta87

Hi, you can use smoove duphold command for exactly this. It will parallelize the samples on a single machine and generate a single VCF for output.

brentp avatar Sep 06 '22 03:09 brentp

Thanks @brentp! My VCF file is already joint genotyped using sniffles2. It seems that smoove will re-genotype the samples (please correct me if I am wrong). My aim is to just annotate my SVs using duphold annotations.

prasundutta87 avatar Sep 06 '22 11:09 prasundutta87