fix: imgag-somatic and integrate seqc2 #63
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… name. Use fixed sample name 'truth' instead.
…notype mismatch rate (#64) * feat: hide genotype_mismatch_rate for somatic reports * feat: function to get info whether somatic or not, edit author * feat: add param somatic to rule render_precision_recall_report_config * feat: hide genotype_mismatch_rate for somatic benchmarking
* feat: add vatools env to allow gt addition * feat: allow gt addition, only works if gt info is missing else Exception * feat: decide between correct contigs and gt-addition, better somatic status extraction * fix: use vcf.gz instead of bcf files for gt addition, use correct callset path * fix: snakefmt on rules * fix: use format string instead of + * fix: change to get(somatic) for somatic status * fix: convert bcf to vcf, add comments
…ng based column and row sorting
…d variants are expected when SNV and indels are in separate files (e.g. STRELKA)
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Waiting for the add-seqc branch to be merged, then we should be good to merge this into main. |
…67) * fix: check if confidence bed is local, target bed gz * add ToDos regarding merge_truthsets * fix: write stratify-truth logs to folder * fix: links to seqc2 datasets * feat: add FORMAT field to truth, fix: change cp to bcftools view -Oz * feat: for somatic truth trigger add_format_field rule * fix: add index to concat snv / indel truthsets * fix: name for seqc2 bm * fix: readable TODO
famosab
changed the title
famosab
changed the title
johanneskoester
approved these changes
Mar 27, 2024
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more to format |
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tests still fail |
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