I'm trying to use bcftools merge to merge vcf files, but am getting the following error:
Incorrect number of FORMAT/fb_AD values at chr14:21499293, cannot merge. The tag is defined as Number=R, but found 3 values and 2 alleles.
I'd love to fix this error, but for a quick fix I'm just trying to remove it. I tried:
bcftools annotate merged_final.vcf.gz -x FORMAT/fb_AD
but then got:
[W::vcf_parse_format] FORMAT 'GT_DISAGREE' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT_SUPPORT' is not defined in the header, assuming Type=String Encountered error, cannot proceed. Please check the error output above.
When I tried to grep the "fb_AD" fromt the file, it is still there:
bcftools view -h merged_final.vcf.gz | grep fb_AD ##FORMAT=<ID=fb_AD_presplit,Number=.,Type=Integer,Description="For the caller fb, (Raw value prior to multiallelic split) Number of observation for each allele"> ##FORMAT=<ID=fb_AD,Number=R,Type=Integer,Description="For the caller fb, Allele depths, calculated from RO and AO tags.">
Not sure how to proceed.