AdamContext.adamVariantContextLoad depends on optional 'contig' header fields when loading a VCF. about adam HOT 7 CLOSED

My opinion is that we probably don't want to fix this one in the current codebase, since the new VCF converter will be available from Mt. Sinai soon.

Additionally, aren't VCFs required to contain contig lines? My understanding is that VCFs without contig lines are illegal.

from adam.

contig entries are not required. From the specification:

As with chromosomal sequences it is highly recommended (but not required) that the header include tags describing the contigs referred to in the VCF file. This furthermore allows these contigs to come from different files. The format is identical to that of a reference sequence, but with an additional URL tag to indicate where that sequence can be found.

from adam.

Ah, the good ol' "highly recommended" cop out...

from adam.

So, if I can summarize the hangout conversation that we (@cyeksig, @fnothaft, @mlinderm, and @nealsid) just had, tell me if this sounds correct:

• Neal is going to make the change from using refId -> referenceName as the primary key, and will break it out as a separate PR
• the regionJoin PR will be blocked on the merging of that PR first
• it will include a way to specify a mapping from "common contig name" to a unique ("full Refseq ID") name at load time, for both BAMs and VCFs.
• Michael will add liftover files that specify those conversions for at least builds 37 and 38 for human

Does that sound about right? Am I forgetting anything? @nealsid, do you want to make this a separate issue? I'll add more comments and thoughts to that, when you create it...

from adam.

Created issue #128 and copied your summary over - thanks Timothy!

from adam.

Thank you, Neal!

On Fri, Feb 21, 2014 at 3:16 PM, Neal [email protected] wrote:

Created issue #128 and copied your summary over - thanks Timothy!

Reply to this email directly or view it on GitHub:
#127 (comment)

from adam.

I am certain this is completely resolved after #238, but believe it was resolved earlier ;).

from adam.