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How to extract sample id using bcftools or vcftools

Dear all,

I am working on vcf data with bcftools. It is a big data set and I would like to see the list of samples are including in this vcf file, what's the easy way with bcftools or vcftools?

Thanks and with best regards

Xinhui

snp vcf bcftools vcftools
• 63,936 views • link
updated by bounlu bounlu • written by xinhui.wang xinhui.wang

What do you mean by the list of samples? If you have a multisample vcf file, you can see the list of samples by looking the names of the columns of vcf file. But maybe I'm misunderstanding your question...

• 0 views • link
written by iraun iraun

Thanks and I would like to get sample ID's in this vcf file. I know we could found at header of vcf file. Is there a parameter in vcftools or bcftools to extract sample ID's?

• 0 views • link
written by xinhui.wang xinhui.wang

2 answers

I got it:

bcftools query -l input.vcf

From manuals - query:

-l, --list-samples: list sample names and exit

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updated by zx8754 zx8754 • written by xinhui.wang xinhui.wang

Oh, I see. Perfect then ;).

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written by iraun iraun

Alternatively you can use vcftools:

vcf-query -l input.vcf
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updated by zx8754 zx8754 • written by bounlu bounlu

vcf-query -l input.vcf, this is not working, could you please give the correct command?

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written by virtualinterlect • virtualinterlect

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