v1.4.1 - Lively Leuven

New Features

1. Added the --output_suffix parameter to add a custom suffix to the basename of the output files.
2. Implemented files for the alphamissense plugin of VEP.
3. Added the --only_pass parameter to only output variants that have the PASS flag in the FILTER column. (This is only applied when --filter is also given)
4. Added the --keep_alt_contigs parameter. This will tell the pipeline to not filter out the alternate contigs, which will now be done by default.
5. Add dbsnp Ids to VCFs coming from vardict. This will be done automatically if a dbsnp VCF is given to the pipeline through the --dbsnp parameter.

Improvements

1. Updated the seqplorer profile so that the output filenames are correct for easy import
2. Changed the separator in --vcfanno_resources to ;
   instead of , to allow commas in glob patterns.
3. Removed the reheader step from the vardict subworkflow and added a simple sed substitution to the vardictjava module
4. vcf2db now uses a python 2 environment to increase it's stability