Hi, firecloud team
I am aligning my WGS with vendor pre-built hg38 reference package, which contains decoy contigs, but not alternate haplotypes and MHC alleles, compared to standard hg38 reference assembly.
I have recently tried running mutect2 and somatic CNV workflow on firecloud for those bams aligned with vendor reference package but assigned firecloud attributes were made from standard hg38 assembly ( I got from Broad data resource bundle, etc). Unfortunately, I have not made it work yet. But not sure whether it is because of different reference used.
Do you suggest using vendor reference for ref_fasta, ref_dict, ref_fai attributes on firecloud? if so, I don't think I can use other reference databases such as PoN, 1000g, gnomad files, because they all made with standard reference build, I think.
Please advise on what I should do.
Thank you very much