keyError: 'gnomAD_AF'

[HomoPolyethylen]

Description of the bug

• querynator uses the gnmoAD allele frequency, annotated by VEP
• VEP annotates the gnomAD AF based on their genomic data or exonic only
• VEP names the fields gnomADg_AF and gnomADe_AF respectively
• there does not seem to be gnomAD_AF anymore (see vep option docs and a search on the vep website yielding no results)

until the issue is fixed in the querynator you can simply alter the annotation field string in your vcf from gnomADg_AF to gnomAD_AF:

bcftools view -Ov INFILE.vcf.gz | sed "s/gnomADg_AF/gnomAD_AF/g" | bcftools view -Oz -o OUTFILE.vcf.gz

Command used and terminal output

No response

System information

No response

[HomoPolyethylen]

apply changes for all samples in samplesheet:

parallel --bar --skip-first-line --colsep , "bcftools view -Ov {2} | sed 's/gnomADg_AF/gnomAD_AF/g' | bcftools view -Oz -o {2}" :::: samplesheet.csv