Ij/complex genotyping

[ionox0]

It appears that we need to figure out a way to add the SHIFT3_ADJUSTED field as an INFO header in the vcf with a type of Integer.

https://github.com/mskcc/ACCESS-Pipeline/pull/251/files#diff-a93c80de4e5a2d19172166846af07399386b4ebcbff465b2ce606f95a994f408R133

Otherwise this fails at the bcftools concat step:

[W::vcf_parse] INFO 'SHIFT3_ADJUSTED' is not defined in the header, assuming Type=String
[E::bcf_translate] Unchecked error (2), exiting
[job bcftools_concat.cwl] completed permanentFail

Once I manually added this to the header, the concat step completed successfully.

I'm not sure how we can use the PyVCF library to add this header though, as I don't see any functionality to add a new header in the API

[ionox0]

Regarding my previous comment, we may be able to use the bcftools reheader command to add the SHIFT3_ADJUSTED INFO field