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CHANGELOG
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CHANGELOG
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***********************************
version-2.4.0
NEW FEATURES
- By default, the bwa mapping now runs in "alt-aware" mode, avoiding multimapped reads in regions of the primary assembly with high
similarities on their alternative contig. Use `-j` in `--bwaOpts` to turn off this function #216, #212
***********************************
version-2.3.0
NEW FEATURES
- Support BAM/CRAM files as input #171, #200
- Generate CRAM files with option --cram
- Add `--step markduplicates` to start the pipeline just after the mapping #207
- 'bwa-mem2' is now the default aligner
SIGNIFICANT USER-VISIBLE CHANGES
- Sambamba is now replaced by GATK/markDuplicates to support CRAM files #171
- Markduplicates has been removed from the filtering step #207
- Tumor only samples without `--msiBaselineConfig` are now ignored (warning) #204
- Minor fixes in MultiQC #203
***********************************
version-2.2.0
NEW FEATURES
- By default, the `work/` folder is now deleted. Use `--disableAutoClean` to turn off this function #183
- Add a filtering step for somatic variants based on VAF/DP/MAF (`--filterSomaticDP`, `--filterSomaticVAF`, `--filterSomaticMAF`)
- New `--skipMutectOrientationModel` option to turn off the learn orientation model step
- Add `--facetsOpts` parameter #168
- Filter out low mapping samples and emtpy VCFs #178
- Add MSIsensor-pro for tumor only samples (`--msiBaselineConfig`) #143
- Add `-profile testwgs` and `-profile testwes` for WES and WGS test set
- Check design file before running the pipeline
SIGNIFICANT USER-VISIBLE CHANGES
- The gene coverage quality controls is now deprecated
- Clean haplotypecaller sub-workflow to remove filtering #176
- Use samtools flagstat for alignment statistics #179
- Sort BAM file on-the-fly in the mapping command #181
- Remove intersection with bed file for WES analysis #159
- Replace all [-. ] in sample name by '_' #163
- Distinguish the annotation of somatic and germline variants
- Speed-up parallel processing and avoid waiting for all the samples at the different steps #158
- Update skip options
- Update Facets outputs #168
- Update mosdepth report in MultiQC #161
- Add `-profile testwes` and `profile testwgs` profiles
BUG FIXES
- Fix bug with HaplotypeCaller for WGS in parallel mode (#175)
***********************************
version-2.1.1
NEW FEATURES
- Add TMB in Tumor Only mode
BUG FIXES
- Bug in --skipFastqc option. Typo in modules.conf
SIGNIFICANT USER-VISIBLE CHANGES
- Bam files after bqsr are exported by default. If --skipBQSR is used, the bams after filering will be exported
***********************************
version-2.1.0
NEW FEATURES
- New --splitFastq and --fastqChunksSize options to split input reads
- Support intervals parallel computing for WGS. See `--noIntervals`
- add '--pon' option for tumor only samples in Mutect2
- Update the calculate contamination process by including the segment files (#143)
- Support bwa-mem2/DRAGMAP mapper (#100, #148)
- Update annotation file for Mutect2 calling
- Update versions of following tools:
- preseq 2.0.3 -> 3.2.0
- samtools 1.10 -> 1.15.1
- bcftools 1.10.2 -> 1.15.1
- picard 2.19.0 -> 2.27.4
- multiqc 1.9 -> 1.13
- mosdepth 0.2.9 -> 0.3.1
- gatk 4.1.6.0 -> 4.1.8.0
- r-base 3.6.3 -> 4.1.3
SIGNIFICANT USER-VISIBLE CHANGES
- Add samtools stats module in the report
- All variants are not returned after filterMutectCall including non PASS ones
***********************************
version-2.0.0
NEW FEATURES
- WARNING - the --interval option is not supported in this version. The processing of WGS can thus be a bit long
- move code to DSL2
- rework of steps. Now 4 functional points of entry in vegan (mapping, filtering, calling and annotate)
- update of SnpEff paremeters
- new tools added: TMB, MSI
- new output files for Facets (ploidy&cellularity file and amp_del file)
- tables listing annotated variants for each sample and for Germline and Somatic variants
- new annotations with SnpSift and COSMIC, ICGC, Gnomad, CancerHotspot and DBNSFP are available
- simplifications of filtering. Now SV and SNVs are filtered the same way
- new parameters to save intermediates BAM, vcf or metrics
- new --ffpe parameter used to specify the TMB threshold
- Mutect2 workflow now includes LearnReadOrientationModel step to
- new parameter --annotDb to define which Databases to use for the annotation step
- update versions of following tools:
- SnpEff & SnpSift 4.3 -> 5.1
- tabix 0.2.6 -> 1.11
SIGNIFICANT USER-VISIBLE CHANGES
- updated documentation and --help message
- refactor outputs
- remove intervals handling for WGS
BUG FIXES
- resolve bug in Facets with output names
***********************************
version-1.2.1
NEW FEATURES
- support for Mouse genome with no population annotation (Mutect2)
***********************************
version-1.2.0
SIGNIFICANT USER-VISIBLE CHANGES
- Update genome conf
- Update mem for Mutect2/bwa-mem
- Update identito output
- Export unfiltered bam files by default
BUG FIXES
- Fix bug in BQSR with targetBed
- Fix bug in 30X coverage for WGS
- Fix mm10 genome
- Update conda identito recipes
- bug in facet with test profile (#102)
***********************************
version-1.1.0
NEW FEATURES
- Add `hg19_base` and `hg38_base` genomes
- Add bcftools norm process
SIGNIFICANT USER-VISIBLE CHANGES
- Move to GATK 4.1.9.0
- Mutect2 fitering now reports only PASS variant (#95)
- Update of the libraries to be less stringent with input parameters
- Update -L option for all GATK process when --targetBed is specified (#95)
BUG FIXES
- Fix bug in apComputePolym.R (#101)
- Mutect2 GetPileupSummaries - fix `-L` option for WES (#95)
- Fix missing conda dependancies in identito
- collectWGSmetrics: use GATK instead of Picard (#98)
**********************************
version-1.0.0
SIGNIFICANT USER-VISIBLE CHANGES
- Move to dbSNP-149 for hg19
- add Facets for CNV calling
- add `--reads` parameter
- add `--singleEnd` option
- Update ressources
- Run BQSR for SNV calling only
- Report reads overlap from picard
- Report insert size distribution with picard
- Add coverage stats with mosdepth
- The design file is now optional
- Update the multiQC report
- Replace --outputDir by --outDir
*********************************
version-0.1.0
NEW FEATURES
- First version of the vegan pipeline