Help with don't have ID when running bcftools annotate

Question

[Chris]

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

Answer 1

[Pierre Lindenbaum]

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

[Chris]

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

[Pierre Lindenbaum]

Replacing the Chr names and position notions in vcf; VCF files: Change Chromosome Notation ; Changing Chromosome Notation On Vcf ; Change chromosome notation to match a new reference ; ....

[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.