How to extract sample id using bcftools or vcftools
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6.4 years ago
xinhui.wang ▴ 400

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 • 28k views
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0
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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...

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0
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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?

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23
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6.4 years ago
xinhui.wang ▴ 400

I got it:

bcftools query -l input.vcf

From manuals - query:

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

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4
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3.6 years ago
Ömer An ▴ 230

Alternatively you can use vcftools:

vcf-query -l input.vcf
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0
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vcf-query -l input.vcf, this is not working, could you please give the correct command?

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You can refer here.

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