mskcc/roslin-variant

Minor updates for post-pipeline scripts

ckandoth opened this issue · 1 comments

ckandoth commented
  • maf_filter.py - Tag mutations that will not be shown in portal. Use the Mutation_Status column in the analysis maf and tag events that are not shown in portal maf with skipped_by_portal.
  • fusion_filter.py - Ensure that merged post-filter SV MAF is created in analysis folder and delivered.
Zuojian-Tang commented

I removed the task below. We will generate .bam.bai file when we insert MSIsensor into roslin:

  • copy_outputs.json - Ensure that .bam.bai files are retained for delivery, in addition to .bai files. The .bam.bai extension is needed for MSIsensor which uses an older htslib.