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M2 Phasing information needs to be integrated into infer ONP #314

Closed LeeTL1220 closed 9 years ago

LeeTL1220 commented 9 years ago

--infer-onp needs to take into account the phasing information.

Basic solution:

  1. Look for phase ID (just check existence) (FORMAT: PGT)
  2. Check (FORMAT: PID) for match between SNPs. The string should be the same if the variants are in the same phase.
LeeTL1220 commented 9 years ago

@ldgauthier @kcibul I need to confirm that the phasing example VCF is also public data. Can one of you confirm?

ldgauthier commented 9 years ago

That's from one of the TCGA LUAD samples. I don't know what the status of that data is.

LeeTL1220 commented 9 years ago

@ldgauthier Then not public.

LeeTL1220 commented 9 years ago

@ldgauthier and @kcibul I anonymized it manually

LeeTL1220 commented 9 years ago

@kcibul and @ldgauthier : Let's say I have two consecutive variants (in genomic space). These are adjacent SNPs. The first has phasing info and the second does not (totally absent). Oncotator will treat this as two separate phases and NOT generate an ONP.

ldgauthier commented 9 years ago

I think that's fine. If the assembly engine isn't confident that they're phased (e.g. reads don't span for whatever reason or the adjacent SNPs weirdly end up in different active regions) then neither am I. Are you concerned about consistency?

LeeTL1220 commented 9 years ago

This was just to confirm. I think that should be treated as a separate phase/allele.

On Fri, Jun 5, 2015 at 11:32 AM, ldgauthier notifications@github.com wrote:

I think that's fine. If the assembly engine isn't confident that they're phased (e.g. reads don't span for whatever reason or the adjacent SNPs weirdly end up in different active regions) then neither am I. Are you concerned about consistency?

— Reply to this email directly or view it on GitHub https://github.com/broadinstitute/oncotator/issues/314#issuecomment-109329967 .

Lee Lichtenstein Broad Institute 75 Ames Street, Room 7003EB Cambridge, MA 02142 617 714 8632

ldgauthier commented 9 years ago

Agreed.

LeeTL1220 commented 9 years ago

@ldgauthier is there ever going to be phasing information on a 0/0 genotype? Just want to confirm...

ldgauthier commented 9 years ago

I'm pretty sure we won't get that information from the assembly. In the highly unlikely event that it's there in some case, we can ignore it for now.