Twist_Solid v0.12.0
Release notes v0.12.0
Version logging
Versions of pipeline, config and softwares used in the analysis are now logged and put into a versions foldor directly under results.
The software versions are obtained by using the inspect function of the signularaties and reports the versions defined by LABEL in the Dockerfile.
The pipeline version is obatined from the github tag/branch.
The combined configfile used in the pipeline is written to one file with added information about software versions for each rule.
The versions info is also gathered and added to MultiQC.
DNA fusions
FuseqWES is now validated with high precision using the new stricter filtering parameters (50 supporting reads). Car should be taken with false positive fusions in amplified genes.
GeneFuse removed as it could not find novel fusions and took long time to run.
Sample mixup test
ID-SNPs is now called also for DNA (before only RNA) using bcftools. For RNA and DNA samples analysed in the same analysis the ID-SNP are compared and the best hit between RNA and DNA is reported in a mixup report. If samples are more than 80% similar it is reported as a match. Unrelated samples are usually around 50% similar while matched samples are typically between 90 and 95% similar.
CNV html report
An extra table is added in the report where 1p19q deletions as well as small deletion and small amplifications candidates are reported.
UMI filter
Slightly updated umi filters. Also updated config for tmb_umi calculations. OBS! TMB is not calibrated for umi yet and will report to high values if not filtered on 5% VAF.
HG38
Reference downloads, designs files and configs updated for hg38.
Changes in config
Changed:
filter_fuseq_wes:
min_support: 50
filter_on_fusiondb: True
tmb_umi: // completely updated
Removed:
gene_fuse:
container: "docker://hydragenetics/genefuse:0.6.1"
report_gene_fuse:
min_unique_reads: 6
scarhrd:
reference_name: "grch37" // moved to hg19 config
vep:
extra: // moved to hg19 config
vep_wo_pick:
extra: // moved to hg19 config
Changes in resources
None
Hydra modules with releases
- prealignment: v1.0.0 (No change)
- alignment: v0.5.0 (No change)
- snv_indels: v0.3.0 (No change)
- annotation: v1.0.1 (No change)
- filtering: v0.3.0 (No change)
- qc: v0.3.0 (No change)
- biomarker: v0.4.0 (No change)
- fusions: v0.1.0 (No change)
- cnv_sv: v0.3.1 (No change)
- reports: v0.4.1 (Now possible to add extra tables in the report)
- misc: v0.2.0 (No change)
Snakemake min version
7.18.0 (no change)
Hydra genetics version
1.14.0 (Updated)
Features
- adapted configs to hg38 (7c601ab)
- added new rule for rna dna mixup check (164baa6)
- cnv html report additional table only includes additional calls (e3971eb)
- data config for HG38 (missing HRD, SVDB, purecn) (7376033)
- increased read support needed for fuseq_wes (f669bc2)
- print pipeline and software version and config to results (d643a39)
- put mixup report directly under result as it is both rna and dna (c9cdbc5)
- removed gene fuse from config (c1f25ba)
- removed gene fuse from pipeline (83260f6)
- update hydra-genetics version (c57d3f3)
- update reports module to v0.4.1 (#398) (32e40e9)
Bug Fixes
- avoid clash with earlier filter annotation (9d2ed1b)
- bug in Snakefile (d8307f4)
- bugfix (a154b11)
- bugfix (75d21be)
- bugfix and improvements (dc7f4b4)
- changed sample mixup från txt to tsv (5b91e60)
- correct paths for CNV report extra tables (#401) (37a461e)
- extra table without tag to cnv html report (765ce51)
- handle missing files better (a0be997)
- make umi tmb similar to tmb (c525c0e)
- min 1% AF (ef2bcaf)
- missing vep config in integration (e8e8a57)
- new smart_open release crash (03e0a0e)
- pycodestyle and unittest update (79cf8f8)
- required variable with corrected indentation (115e018)
- resolve conflicts (6343bd2)
- rm dangerous qual filter form umi (c9d4584)
- rm dangerous qual filter form umi (d20f0cc)
- some hg19 file leftovers fixed (5433b16)
- VEP cache move to config.data (a36b570)