feat: reports of benchmarking somatic variant calling now hide the genotype mismatch rate #64
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johanneskoester
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Mar 28, 2024
* feat: add imgag somatic benchmark datasets to presets * feat: add param for somatic benchmarking to presets * feat: add squash-ploidy to benchmark_variants for somatic calls * fix: use input function for somatic param * feat: test for imgag somatic benchmark * feat: add workflow_dispatch to run tests on other branches * fix: lookup benchmark with correct benchmark name instead of callset name * fix: format common and eval locally with snakefmt * feat: add new param tumor_sample_name to config * feat: add rule to extract truth sample name to eval * feat: expand get_somatic_flag by truth and callset sample name * fix: missing ':' in function * fix: get fix for f-strings from main * Test: Try to trigger extract_truth_sample_name * feat: set sample name to 'truth' for generated truth vcf * fix: remove non working rule and function for extracting truth sample name. Use fixed sample name 'truth' instead. * fix: stop overwriting sample names in header of callset * feat: reports of benchmarking somatic variant calling now hide the genotype 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 * fix: add else statement to not hide genotype mismatch for germline * feat: add genotype field to vcf if missing to run rtg vcfeval (#65) * 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 * fix detection whether dataframe can be used for hierarchical clustering based column and row sorting * Fix: remove value error in collect_stratifications, since no predicted variants are expected when SNV and indels are in separate files (e.g. STRELKA) * fix: switch back to bcf files see #66 * fix: switch back to bcf files see #66 * fix: ignore log folder * fix: modify links and add FORMAT field to make seqc2-somatic bm work (#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 * fix: snakefmt on common * fix: unused info in config * fix: snakefmt on eval * fix: add tumor_sample_name to test config * test: remove giab and chm test * test: remove imgag add giab * test: remove giab and add chm * test: add seqc2 and comment giab * fix: dummy seqc2 --------- Co-authored-by: Johannes Koester <[email protected]> Co-authored-by: BiancaStoecker <[email protected]>
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