Question: How to extract sample id using bcftools or vcftools
3
gravatar for xinhui.wang
3.6 years ago by
xinhui.wang150
Netherlands
xinhui.wang150 wrote:

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 vcftools bcftools vcf • 9.9k views
ADD COMMENTlink modified 20 days ago by zx87546.0k • written 3.6 years ago by xinhui.wang150

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...

ADD REPLYlink written 3.6 years ago by iraun3.5k

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?

ADD REPLYlink written 3.6 years ago by xinhui.wang150
9
gravatar for xinhui.wang
3.6 years ago by
xinhui.wang150
Netherlands
xinhui.wang150 wrote:

I got it:

bcftools query -l input.vcf

From manuals - query:

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

ADD COMMENTlink modified 20 days ago by zx87546.0k • written 3.6 years ago by xinhui.wang150
2
gravatar for bounlu
9 months ago by
bounlu170
Singapore
bounlu170 wrote:

Alternatively you can use vcftools:

vcf-query -l input.vcf
ADD COMMENTlink modified 20 days ago by zx87546.0k • written 9 months ago by bounlu170
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