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error on extracting a snp from vcf file using bcftools

Hello,

I am trying to extract a SNP based on POS column from a multisample vcf file.
I need the entire line with all the calls for all samples for the respective SNP.
I used:

bcftools view --include POS==41766 input.vcf -o SNP_41766

But the output file shows vcf header only.
Thank you for any help!

snp
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updated by Medhat Medhat • written by evafinegan • evafinegan

Hi, it should work as you are running it. Are you sure that there is a record at this position? What if you simply grep the line:

bcftools view input.vcf | grep -P "\t41766\t"

Note that you can also extract the header with grep by using:

bcftools view input.vcf | grep -P "\t41766\t|^#"

Note: if your VCF is indeed uncompressed, then this will also work:

grep -P "\t41766\t" input.vcf
grep -P "\t41766\t|^#" input.vcf
• 0 views • link
written by Kevin Blighe Kevin Blighe

That will select only the variant in chr1, but I think the question refers to all events.

• 0 views • link
written by Medhat Medhat

Hello everyone! Thank you for your suggestions! I tried most of the suggestions but it is weird that I am still getting the header only (not the desired SNP row).

• 0 views • link
written by evafinegan • evafinegan

Any error? maybe try to use other position if you did not already, make sure you copy it from your vcf file.

• 0 views • link
written by Medhat Medhat

1 answer

To use bcftools, I would write it in this the way:
bcftools view --include 'POS=41766' input.vcf -o SNP_41766

This also will work, but I prefer the previous one:
bcftools view --include POS=41766 input.vcf -o SNP_41766

• 0 views • link
written by Medhat Medhat

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