bcftools error on freebayes vcfs

Question

[mark.rose]

Hi

When attempting to run bcftools merge (v1.9) on freebayes (v1.3.4) vcfs I get the following error:

Incorrect number of FORMAT/AD values at <fasta>:1325, cannot merge. The tag is defined as Number=R, but found 3 values and 2 alleles.

Posted on the freebayes Google Group but no response.

Help would be appreciated.

Thanks
Mark

Answer 1

[iraun]

Hi!

I had this problem in the past and I solved it by replacing VCF header for AD field from Number=R to Number=.

Fyi, in my case the source of the error was having more AD fields than REF and ALT alleles due to some VCF pre-processing.