Question

Chromosome lost after merge with vcf-merge

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6.3 years ago

boymin2020 ▴ 80

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 • 1.5k views

ADD COMMENT • link 6.3 years ago by boymin2020 ▴ 80

score 1 · Answer 1 · 2018-08-17

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6.3 years ago

Kevin Blighe 88k

vcf-merge is outdated.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

ADD COMMENT • link 6.3 years ago by Kevin Blighe 88k

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

ADD REPLY • link 6.3 years ago by boymin2020 ▴ 80

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So, the question is resolved?

ADD REPLY • link 6.3 years ago by Kevin Blighe 88k

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Yes. Thanks for the follow-up.

ADD REPLY • link 6.3 years ago by boymin2020 ▴ 80

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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 REPLY • link 6.3 years ago by Kevin Blighe 88k