Closed PedalheadPHX closed 5 years ago
Yes. Ryan implemented the filtering using SnpSift.
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.
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I'm guessing that is the project that we were monkeying with yesterday. We added the filtering step as a separate task to Phoenix:
I kicked off the COLO and UTJMM projects again to test the latest changes:
/scratch/rrichholt/Phoenix-376ec6f
So even though the filtering is possible within vcfMerger2 tool, Ryan did implement a vcfMerger2-independent filtering process in the pipeline.
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"