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using duphold on a multisample trio VCF file #48

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prasundutta87 opened this issue Sep 5, 2022 · 2 comments
Open

using duphold on a multisample trio VCF file #48

prasundutta87 opened this issue Sep 5, 2022 · 2 comments

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@prasundutta87
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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
@brentp
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brentp commented Sep 6, 2022

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.

@prasundutta87
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prasundutta87 commented Sep 6, 2022 •
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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.

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@brentp @prasundutta87