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Help with don't have ID when running bcftools annotate

Hi all,

I don't know why I run similar command with the previous one I ran but I don't get the ID this time. The only thing I change is the vcf from another tool. Would you please have a suggestion? Thank you so much!

bcftools annotate -a /00-All.vcf.gz -c ID -o /sarek_ID.vcf.gz /variant_calling/deepvariant/sample_1/deepvariant.vcf.gz
bcftools
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written by Chris • Chris

1 answer

I bet your chromosomes do not use the same notation ( 'chr1' vs '1')

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre! I used nf-core pipeline to get the vcf file this time, so how can I fix this?

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written by Chris • Chris

I checked the vcf file before and after running the command, it used the notation chr1. The vcf which successfully add ID used the notation 1.

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written by Chris • Chris

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