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 theMutation_Status
column in the analysis maf and tag events that are not shown in portal maf withskipped_by_portal
. -
fusion_filter.py
- Ensure that merged post-filter SV MAF is created inanalysis
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.