How to extract sample id using bcftools or vcftools

Question

[xinhui.wang]

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

[iraun]

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...

[xinhui.wang]

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?

Answer 1

[xinhui.wang]

I got it:

bcftools query -l input.vcf

From manuals - query:

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

Answer 2

[Ömer An]

Alternatively you can use vcftools:

vcf-query -l input.vcf

[virtualinterlect]

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

[Ömer An]

You can refer here.