This repository has been archived by the owner on Aug 23, 2024. It is now read-only.
- Update base image to dockstore-cgpwxs:3.1.6 (from 3.0.3)
- Includes, memory footprint reduction for Caveman flagging
- Significant speedup in indel input generation
- Parallel flagging for SNV
- Fragment based SNV/Indel calling
- Upgrade allele counter and brass
- Reduce number of layers in final image.
- Remove some legacy env vars from wrappers
- Battenberg removed
- Was only included to do base allele counts not complete analysis
- Underlying data files are not supported for new builds or other species
- Contact original authors for ongoing support
- Wrapper script didn't explicitly specify sex SNP loci file (ASCAT)
- no impact for GRCh37 other species/build would have used wrong sex chromosome SNPs
- CaVEMan step wasn't being passed normal contamination value, scientific impact:
- previously
caveman.pldefault of0.1was applied - this will now honor the value from ASCAT (
1-$rho)
- previously