grch37-lite in Call Somatic Mutations WGS
TARGET WGS data was aligned to GRCH37-lite. Internally, GP has aligned to Hg19. Is there a easy way to merge the two together without having to realign the TARGET data (and take up a lot of space realigning)?
I ask since I'm trying to use Call Somatic Mutations WGS in firehose but because GRCH37-lite is slightly simplified, there are contigs that are missing and thus the process fails.
Alternatively, are there annotations somewhere for the GRCH37-lite that I could use? I don't see it on Algorithms Commons.
(Sorry if this is an over simplification... I'm still pretty new to this)