search

tgen / vcfMerger2

Dynamic vcfMerger for 2 to N somatic variants vcf files
Other
5 stars 1 forks source link

Filtering Occuring? #3

Closed PedalheadPHX closed 5 years ago

PedalheadPHX commented 5 years ago

Is vcfMerger doing filtering in the pipeline?

UTJMM merged VCF header

STRELKA2_SnpSiftCmd="SnpSift Filter '(GEN[ALL].DP > 10) & (GEN[0].AR < 0.02 & GEN[1].AR > 0.05)' temp/vcfmerger2/UTJMM_0008_3_PB_Whole_C1_KHSTL-UTJMM_0008_2_BM_CD138pos_T1_KHSTL/UTJMM_0008_3

_PB_Whole_C1_KHSTL-UTJMM_0008_2_BM_CD138pos_T1_KHSTL_bwa_strelka2.prepz.vcf"

ChristopheLegendre commented 5 years ago

Yes. Ryan implemented the filtering using SnpSift.

PedalheadPHX commented 5 years ago

I don’t want that process hidden in another step, needs to be a stand alone thing

For the tool these kinds of wrapper functions will cause you nothing but issues when it goes public and people chose to use it

On Thu, May 2, 2019 at 01:45 Chris notifications@github.com wrote:

Yes. Ryan implemented the filtering using SnpSift.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/tgen/vcfMerger2/issues/3#issuecomment-488594271, or mute the thread https://github.com/notifications/unsubscribe-auth/AC6VCHDL26SE4NDTTCWUHT3PTKSY7ANCNFSM4HJ3UTOA .

-- Sent from a mobile device

--

This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

ryanrichholt commented 5 years ago

I'm guessing that is the project that we were monkeying with yesterday. We added the filtering step as a separate task to Phoenix:

https://github.com/tgen/phoenix/blob/376ec6f703194b30e28435c1f0a3fb7b0c383d1b/modules/somatic/vcfmerger2.jst#L52-L69

I kicked off the COLO and UTJMM projects again to test the latest changes:

/scratch/rrichholt/Phoenix-376ec6f

ChristopheLegendre commented 5 years ago

So even though the filtering is possible within vcfMerger2 tool, Ryan did implement a vcfMerger2-independent filtering process in the pipeline.