Question: Chromosome lost after merge with vcf-merge
0
gravatar for boymin2020
2.1 years ago by
boymin202020
boymin202020 wrote:

Hi all,

I have merged a number of WGS VCF files generated from the standard GATK pipeline with vcf-merge function of VCFtools. The merged big VCF file shows that the chromosomes after 19 (e.g., Chrom20) lost. I guess one/some individual VCF files do(es) not have the lost chroms. Are there any possibilities?

Bests

vcf-merge • 581 views
ADD COMMENTlink written 2.1 years ago by boymin202020
1
gravatar for Kevin Blighe
2.1 years ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

vcf-merge is outdated. Can you retry with bcftools merge ? Also please paste the commands that you have used.

ADD COMMENTlink written 2.1 years ago by Kevin Blighe65k

Thanks for your advice. bcftools merge works much faster and very well.

ADD REPLYlink written 2.1 years ago by boymin202020

So, the question is resolved?

ADD REPLYlink written 2.1 years ago by Kevin Blighe65k

Yes. Thanks for the follow-up.

ADD REPLYlink written 2.1 years ago by boymin202020

Great. I've moved my comment to an answer, to help others. To re-iterate: BCFtools should be used in place of VCFtools in the future.

ADD REPLYlink written 2.1 years ago by Kevin Blighe65k
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