feat: add TIDDIT tumor normal filtering #1120
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…val of duplicate instances of BND variants
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## develop #1120 +/- ##
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Coverage 99.31% 99.31%
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…er rule after svdb merge
BALSAMIC/snakemake_rules/variant_calling/somatic_sv_quality_filter.rule
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…dless of normal presence
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BALSAMIC/snakemake_rules/variant_calling/somatic_sv_quality_filter.rule
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…IC into feat_filter_SVs
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### Added: * PIP specific missing tools to config #1096 * Filtering script to remove normal variants from TIDDIT #1120 * Store TMB files in HK #1144 ### Changed: * Fixed all conda container dependencies #1096 * Changed --max_sv_size in VEP params to the size of chr1 for hg19 #1124 * Increased time-limit for sambamba_exon_depth and picard_markduplicates to 6 hours #1143 * Update cosmicdb to v97 #1147 * Updated read the docs with the changes relevant to mention #1153 ### Fixed: * Update cryptography version (39.0.1) due to security alert #1087 * Bump cryptography to v40.0.2 and gsutil to v5.23 #1154 * Pytest file saved in balsamic directory #1093 * Fix varcall_py3 container bcftools dependency error #1097 * AscatNgs container #1155
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This PR:
Aims to reduce the number of structural variants in the final SV & CNV VCF.
Currently solely by adding filters to the TIDDIT rules which removes SVs that have been called in the normal sample as well (only relevant for WGS tumor normal analyses).
Added: for new features.
Further information about implementation and testing can be found in this issue: #1119
And this discussion: #1127
Tests done
The only type of analyses running the rule affected by this change is WGS T / N.
Review and tests: