Help with don't have ID when running bcftools annotate
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17 months ago
Chris ▴ 340

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 • 842 views
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17 months ago

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

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

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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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