Add soft filter tags

• Stopped running filter_vaf.R and filter_cohort_normals.R
• Added soft filter tags: nad3, and asb
• Added MuTect-Rescue tag if set column becomes empty under certain conditions
• Fixed bugs when no counts for normal panel occurrences

Better normal_panel, stricter repeat_masking

• normal_panel now tags events in >=5 normals at VAFs >1/10th the VAF (min 0.1%) observed in tumor
• Fixed a bug where tags were not applied if FILTER was blank, and hence NA in the data.table
• Indels and MNPs now need to be fully contained within a repeat/blacklisted region to be tagged
• Rename dmp_filter to vaf_filter since we use different cutoffs than DMP does

Tweak for more sensitivity in WES and IMPACT

• Loosen dmp_filter from minimum t_alt_count 8 to 3 for hotspots, and 5 for non-hotspots.
• Remove likely FP hotspots per gnomAD from the hotspot list.
• Exclude the low_confidence filter from run_ngs-filters.py due to high false negative rates.
• The normal_panel filter now requires at least 5 samples to support the event (earlier 3).
• Fixed incorrect version numbers in the output MAF header lines.

Cyriacattack

• Removed pandas from requirements.txt
• Tossed FFPE filters because they did bad, will implement a better one later
• Use fewer intermediate MAFs to reduce disk usage
• Use /scratch/ instead of /tmp for temp MAFs
• Replace PASS with new FILTER tags, rather than appending tags to PASS
• Uses ";" as delimiter for tags instead of "," per VCF specs for FILTER field

First Release after Jenkins Test worked

Version 1.1.3

Fixes for filter_ffpe.R

Version 1.1.2

Bug fix to repeat masker bed to protect TERT promoter.

Version 1.1.1

Added apply filter wrapper script

Version 1.0.1

First version rolled into BIC Variants Pipeline