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add INFO tag to vcf with bcftools

My vcf is missing the CIPOS tag and i would simply like to add CIPOS=0,0 to all records. I am having trouble executing this with bcftools

> bcftools annotate -c INFO/CIPOS="0,0" -o out.vcf in.vcf
The tag "CIPOS=0" is not defined in (null)
> bcftools annotate -c CIPOS=0,0 -o out.vcf in.vcf
The tag "CIPOS=0" is not defined in (null)
> bcftools annotate -c INFO/CIPOS -o out.vcf in.vcf
The tag "CIPOS" is not defined in (null)

Do I have to create another file? Is this because CIPOS is not defined in the header and I have to manually add it there?

Update: Adding a line to the header does prevent non-zero exit, but the default value I want is not added

echo "##INFO=<ID=CIPOS,Number=2,Type=Integer,Description=\"Confidence interval around POS\">" > hdr.txt
bcftools annotate -h hdr.txt  -c CIPOS -o out.vcf in.vcf

Even with hdr.txt, i cannot explicitly set the value.

bcftools vcf
• 1,958 views • link
updated by Ram Ram • written by from the mountains from the mountains

1 answer

This is not how bcftools annotate works. Please read the examples in the documentation to understand how to use -c - you will need -a as well.

I think the easiest thing to do in your case would be to add a header line manually then use awk to add CIPOS=0,0; to $8.

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written by Ram Ram

gotcha! thanks. this seems to be a little less straightforward than I had hoped but also not overly complicated. I simply used reheader and concatenated CIPOS to each INFO field using awk.

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updated by Ram Ram • written by from the mountains from the mountains

Hi, I'm trying to do something similar, could you share the code to do what you describe.

Thanks

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updated by Ram Ram • written by Javier • Javier

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