Question: how to extract sample id with bcftools or vcftools
2
gravatar for xinhui.wang
3.4 years ago by
xinhui.wang140
Netherlands
xinhui.wang140 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 • 8.8k views
ADD COMMENTlink modified 6 months ago by bounlu140 • written 3.4 years ago by xinhui.wang140

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 3.4 years ago by iraun3.4k

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 3.4 years ago by xinhui.wang140
9
gravatar for xinhui.wang
3.4 years ago by
xinhui.wang140
Netherlands
xinhui.wang140 wrote:

thanks. I got it

bcftools query -l input.vcf

ADD COMMENTlink written 3.4 years ago by xinhui.wang140

Oh, I see. Perfect then ;).

ADD REPLYlink written 3.4 years ago by iraun3.4k
0
gravatar for bounlu
6 months ago by
bounlu140
Singapore
bounlu140 wrote:

alternatively you can use vcftools:

vcf-query -l input.vcf

ADD COMMENTlink written 6 months ago by bounlu140
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