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tgen / phoenix

Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
MIT License
16 stars 6 forks source link

Test Samtools Optical Dups - current build #173

Closed PedalheadPHX closed 4 years ago

PedalheadPHX commented 4 years ago

@TGEN-BTurner Is there a run complete with this that I can review?

bryce-turner commented 4 years ago

Although likely not optimal to gather a conclusion from, TPRC_0014 and TPRC_0015 both are completed projects that had markdups. Here is the path to the stats of TPRC_0015: /scratch/tgenjetstream/centro/projects/TPRC_0015_248a9dccfe/exome/alignment/bwa/TPRC_0015_1_PB_Whole_C1_KHSTX/stats

The recently running MMRF projects should have markdups completed by now, but the projects themselves are still pending. Here is the path one of those directories: /scratch/tgenjetstream/centro/projects/MMRF_1061_248b284651/genome/alignment/bwa/MMRF_1061_1_BM_CD138pos_T2_TSWGL/stats

PedalheadPHX commented 4 years ago

Looks to be working, oddly no @PG lines even though there is a --no-PG option now.