using duphold on a multisample trio VCF file

brentp / duphold

don't get DUP'ed or DEL'ed by your putative SVs.

MIT License

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using duphold on a multisample trio VCF file #48

Open prasundutta87 opened 2 years ago

prasundutta87 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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.