Is it possible to get the contig list for VCF records?

NCBI-Hackathons / NovoGraph

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

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Is it possible to get the contig list for VCF records? #21

Closed JYLeeBioinfo closed 4 years ago

JYLeeBioinfo commented 5 years ago

Hello!

I want to find contigs for individual rows of output VCF, so that I can identify the sample from which they are originated.

If I can get the list of contigs that generated a specific VCF record, I will be able to identify the sample.

Is there an option to do this task?

Thank you Jinyoung

evanbiederstedt commented 4 years ago

Hi @hd00ljy

Apologies for the delay.

I may be misunderstanding---you would like that information written into a VCF column? I think for the VCFs we generated for the paper, that information existed. It depends on the contig names in the input BAMs.

https://osf.io/3vs42/?view_only=fedd8437d96c4d688f6c40150903d857

Let me know if the information you desire is included in the VCFs above. If so, I think that answers you inquiry (but I could be confused as well).

Thanks, Evan

evanbiederstedt commented 4 years ago

I think this is resolved.