feat: add TIDDIT tumor normal filtering #1120

Merged

mathiasbio merged 47 commits intodevelopfrom feat_filter_SVs

Apr 26, 2023

+488-7

Commits on Mar 24, 2023

adding rough filtering of variants present in normal sample, and removal of duplicate instances of BND variants
mathiasbio
committed
adding removal of duplicate instances of BND variants in tumor only tiddit
mathiasbio
committed

Commits on Mar 28, 2023

fix bug, add rescuecontam vcf to vcfdir for testing purposes
mathiasbio
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correct bcftools commands
mathiasbio
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move tumor normal filtering from tiddit rule to bcftoosl quality filter rule after svdb merge
mathiasbio
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Commits on Mar 30, 2023

Commits on Apr 4, 2023

increase the minimum overlap for merging tumor and normal tiddit variants to 0.8
mathiasbio
committed

Commits on Apr 5, 2023

add filter which preserves all BNDs with presence in the tumor, regardless of normal presence
mathiasbio
committed

Commits on Apr 13, 2023

adding wip sv_filter script, adding no_intra option to merge tiddit svdb
mathiasbio
committed

Commits on Apr 17, 2023

Commits on Apr 18, 2023

Commits on Apr 19, 2023

Commits on Apr 25, 2023