QC metrics

[tanglingfung]

(sorry, I am still using variant, instead of varinat2 pipeline)

duplicates metrics is not correctly reported since it's trying to get this information from the recalibrated realigned bam (which has already had duplicates removed). I would actually prefer 'mark duplicates' to 'duplicates removal' in the earlier step

[chapmanb]

Paul;
Sorry, this one slipped by me and I meant to check in the fix earlier. Apologies. Hope this fixes it for you.

More generally, can you remind me what is holding up the move to variant2 from your perspective? I am thinking about deprecating and removing the older pipeline, so want to understand what features it has that variant2 lacks.

[tanglingfung]

Hi Brad,

no problem. I should have looked into the issue as well, but a bit occupied
with other work.

I'm switching over to variant2 pipeline as well. But I kind of want to
retain the variant pipeline in case my 'old' projects need to add 1-2
samples and I don't need to re-run everything all over again.

I am stuck at the GEMINI QC metrics right now, but I also tried to use GATK
or plinkseq to by-pass this step.

Thanks again for all of your help.

Paul

On Mon, Jul 8, 2013 at 8:52 AM, Brad Chapman notifications@github.comwrote:

Paul;
Sorry, this one slipped by me and I meant to check in the fix earlier.
Apologies. Hope this fixes it for you.

More generally, can you remind me what is holding up the move to variant2
from your perspective? I am thinking about deprecating and removing the
older pipeline, so want to understand what features it has that variant2
lacks.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/35#issuecomment-20615284
.

[tanglingfung]

and i thought you have special reason to remove the duplicates from the bam. Your fix is the way I used to by-pass the issue.