Annotation of germline MAF

[kpjonsson]

Per planning meeting 6/26, we will limit annotation of the germline MAF to:

• ClinVar ~_(VEP annotation does add ClinVar but we might need to investigate whether it's sufficient: https://useast.ensembl.org/info/docs/tools/vep/script/vep_custom.html)_~

  • More detailed ClinVar annotation can be retrieved as described above, either as a plugin to VEP or by annotation using bcftools annotate. However, the list of variants in the raw VCF ClinVar provides contains all variants (i.e. cancer and non-cancer disease associated). I couldn't find a good way to subset on those variants only implicated in cancer, so for now I'm gonna settle with the VEP annotation vcf2maf provides.

• BRCA exchange:

  • This is done using https://github.com/taylor-lab/annotateMaf

[evanbiederstedt]

@kpjonsson

This is done using https://github.com/taylor-lab/annotateMaf

I think we should probably containerize this, no? Would you prefer a new process?

[kpjonsson]

@kpjonsson

This is done using https://github.com/taylor-lab/annotateMaf

I think we should probably containerize this, no? Would you prefer a new process?

This is already implemented here: https://github.com/mskcc/vaporware/blob/ab87c4d59a8d80b86f1bb31cf788fffd7d868698/pipeline.nf#L2166.