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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

Develop

  • Adds loqudb and gnomad frequencies to vcf2cytosure filtering
  • Store PCT_PF_READS_IMPROPER_PAIRS in qc file
  • Evaluate and fail analysis where PCT_PF_READS_IMPROPER_PAIRS is above 5 %

[12.0.0]

  • Set overlap requirement for merging two SVs to 0.8, down from the 0.95 default
  • Set overlap requirement for SV annotation to 0.6, up from 0.5
  • Update Tiddit to improve SV positioning
  • Increased memory allocation for salmon and picardtools_mergersamfiles (RNA)
  • New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
  • Remove the RSeQC read duplication analysis as it often fails.
  • Increased run time allocation for gatk_asereadcounter.
  • Increased the default required length for a trimmed rna read to be retained from 20 bp to 40 bp. Configurable via CLI or config.
  • Fixed a bug where gnomad SV version 2.0 instead of version 2.1 was used to annotate SVs
  • One-pass instead of two-pass mapping with STAR-Fusion, as recommended for STAR-Fusion 1.12
  • Bump max run time for retroseq to 15 hours.

Tools

  • Arriba 2.3.0 -> 2.4.0
  • DeepVariant 1.4.0 -> 1.5.0
  • FastQC: 0.11.9 -> 0.12.1
  • GATK: 4.2.6.1 -> 4.4.0.0
  • Gffcompare 0.11.2 -> 0.12.6
  • Htslib 1.15.1 -> 1.16
  • MegaFusion 66a3a80 -> d3feacf
  • Picard 2.27.2 -> 2.27.5
  • STAR-Fusion 1.11.0 -> 1.12.0
  • SVDB: 2.7.0 -> 2.8.2
  • Tiddit 3.3.2 -> 3.6.0

Databases

clinvar: 20220829 -> 20230508 loqusdb snapshot: 20230208 -> 20230512 hmtvar: oct2022

[11.2.2]

  • New patch of gens pre processing container.

Tools

  • gens_preproc 1.0.8 -> 1.0.11

[11.2.1]

  • Patching of gens pre processing container to solve an issue with incomplete bed files.

Tools

  • gens_preproc 1.0.2 -> 1.0.8

[11.2.0]

  • Adds retroseq for mobile element detection

Databases

  • expansionhunter variant catalog: v4.0.2 -> v5.0.0

Tools

  • RetroSeq: 9d4f3b5

[11.1.3]

  • Adds Gens' bed index file to deliverables

[11.1.2]

  • Fixed a bug in the mitochondrial deletion recipe affecting samples with 0 intermediate discordant MT reads.

[11.1.1]

  • Updates chromgraph to version 1.3.1
  • Added vcfanno config version 1.18 to the download config

[11.1.0]

  • Save raw files from ExpansionHunter
  • Run UPD and subsequently chromograph on unaffected children
  • Annotate SV variants with the caller that reported the variant
  • Produce files for CNV analysis in Gens
  • Updated SO terms for new version of VEP
  • ExACpLI -> pLI, see vep issue 108
  • Use REVEL_score rather than REVEL_rankscore for the ranking algorithm
  • Use BWA-mem2 instead of BWA mem for mapping
  • Set default annotation overlap for structural variants to 0.5 (previously 0.8), due to change in TIDDIT
  • Turn on Stringtie and gffcompare by default
  • Run varg on research vcf
  • Increase max for coverage calculation to 500x
  • Separate list of ranked SO terms for structural variants to ensure that the right SO term gets picked as the most severe for SVs
  • Adds option to use bedpe files with svdb query

Tools

  • Arriba: 2.1.0 -> 2.3.0
  • Chromograph 1.1.4 -> 1.3.0
  • DeepVariant: 1.1.0 -> 1.4.0
  • ExpansionHunter: 4.0.2 -> 5.0.0
  • GATK: 4.2.2.0 -> 4.2.6.1
  • HTSlib: 1.13 -> 1.15.1
  • MultiQC: 1.11 -> 1.12
  • Peddy: 0.4.3 -> 0.4.8
  • Picard: 2.25.0 -> 2.27.2
  • SMNCopyNumberCaller 1.1.1 -> 1.1.2
  • Star Fusion: 1.10.1 -> 1.11.0
  • Stranger: 0.8.0 -> 0.8.1
  • Stringtie: 2.1.3b -> 2.2.1
  • Tiddit: 2.12.1 -> 3.3.2
  • Trimgalore: 0.6.4 -> 0.6.7
  • VEP: 104.3 -> 107.0
  • svdb: 2.4.0 -> 2.7.0
  • vcf2cytosure v0.5.1 -> v0.8

Databases

  • clinvar: 20211010 -> 20220829
  • dbnsfp: 4.1a -> 4.3a (grch38 only)
  • gnomad: r3.1.1 -> r3.1.2 (grch38 only)
  • giab: 3.3.2 -> 4.2.1
  • loqusdb dump: 20210921 -> c
  • nist: v3.3.2 -> v4.2.1
  • vcf2cytosure blacklist: 200520

[11.0.3]

  • Initiate conda prior to activation

[11.0.2]

Updates chromograph

Tools

chromograph 1.1.4 -> 1.1.5

[11.0.1]

  • When running Deepvariant, set tmpdir to analysis folder and use intermediate_results_dir.
  • When running DeepVariant via singularity, use the options --no-home and --cleanenv.

[11.0.0]

  • HmtNote: annotate mitochondrial variants in VCF file
  • Updating to latest and greatest versions
  • Mitochondrial deletion analysis
  • GATK Haplotypecaller has been turned off in favour of Deepvariant
  • Introduces possibility to store singularity images locally as a .sif file
  • Increased allele frequency cut off for when a variant is filtered out to 0.7
  • Turned off Star_caller and Telomerecat by default

Tools

  • cyrius v1.1 -> v1.1.1
  • deepvariant 1.1.0 -> 1.2.0
  • deeptrio 1.1.0 -> 1.2.0
  • gatk 4.2.0.0 -> 4.2.2.0
  • glnexus v1.3.1 -> v1.4.1
  • HmtNote: 0.7.2
  • htslib: 1.10.2 -> 1.13
  • multiqc 1.10.1 -> v1.11
  • star-fusion 1.10.0 -> 1.10.1
  • vep release_103.1 -> release_104.3

References

  • gnomad: r3.0 -> r3.1.1
  • [NEW] gnomad mt: r3.1
  • clinvar: 20210415 -> 20211010

[10.2.5]

  • Allow slurm quality of service flag to be set to 'express'

[10.2.4]

  • Split Star-Fusion alignment and detection into two recipes
  • Use temp directory with Star-Fusion
  • Resource bump for RNA
  • Limit memory for glnexus
  • Use non-gpu version of Deepvariant by default

[10.2.3]

  • Updates Chromograph to version 1.1.4

[10.2.5]

  • Allow slurm quality of service flag to be set to 'express'

[10.2.4]

  • Split Star-Fusion alignment and detection into two recipes
  • Use temp directory with Star-Fusion
  • Resource bump for RNA
  • Limit memory for glnexus
  • Use non-gpu version of Deepvariant by default

[10.2.3]

  • Updates Chromograph to version 1.1.4

[10.2.2]

  • Adds missing median coverage metrics to metrics deliverable file

[10.2.1]

  • Removed frequency filtering for mitochondrial sites

[10.2.0]

  • Introduced the option --start_after_recipe <recipe_name> to start the pipeline after a given recipe

[10.1.0]

  • Only store qc_metrics_deliverables path in file store for downstream parsing

[10.0.3]

  • Remove duplicates from Glnexus output

[10.0.2]

  • Glnexus are used to genotype the gvcf regardless of how many samples that are analysed.
  • Resource bump to the MIP RNA recipe fusion_report

[10.0.1]

  • Fix to gene panel regexp
  • Use automated build of MIP
  • Increased memory allocation for version_collect

Tools

stranger: 0.7.1 -> 0.8.0

[10.0.0]

  • Remove unused recipe split_fastq_file
  • Align with the same bwa mem options as used by Broad
    • Fixed number of bases in each batch
    • Use bwa mem instead of run-bwamem for alignment to grch38
  • Use Chanjo repos Docker file instead of MIPs
  • Removed support to run bcftools_mpileup as a variant caller
  • Added perl and MIP docker file and use it in recipes
  • Removed PATH check for proxy bins
  • Switched to using container manager instead of proxy bins in recipes
  • Removed support to run variant_integrity
  • Added deepvariant as variant caller and glnexus to merge samples to case vcf

Tools

arriba: v1.2.0 -> v2.1.0 bedtools: 2.29.0 -> 2.30.0 bwa-mem2 2.0 -> 2.2 chanjo: 4.2.0 -> 4.6 chromograph: 1.0.1 -> 1.1 cyrius: v1.0 -> v1.1 deepvariant: 1.1.0 delly: 0.8.1 -> 0.8.7 gatk: v4.1.8.1 -> v4.2.0.0 glnexus: v1.3.1 megafusion: 66a3a80 multiqc: 1.9 -> 1.10.1 pdfmerger: v1.0 picardtools: 2.23.4 -> 2.25.0 preseq: 2.0.3 -> 3.1.2 rseqc: 3.0.1 -> 4.0.0 rtg-tools: 3.10.1 -> 3.12 salmon: 0.12.0 -> 1.4.0 smncopynumbercaller: 4b2c1ad -> v1.1.1 star: 2.7.4a -> 2.7.8a stranger: 0.7 -> 0.7.1 svdb: 2.2.0 -> 2.4.0--py37h77a2a36_4 tiddit: 2.8.1 -> 2.12.1 upd: 0.1 -> 0.1.1

References

  • clinvar_20200905 -> clinvar_20210415
  • VEP cache: 100 -> 103.1
  • grch37_gencode_v19_ctat_lib_plug-n-play_-apr032020-.tar.gz -> grch37_gencode_v19_CTAT_lib_Mar012021.plug-n-play.tar.gz
  • grch38_gencode_v31_ctat_lib_plug-n-play_-apr062020-.tar.gz -> grch38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz
  • gencode annotation: v34 -> v37

[9.1.3]

  • Fix memory allocation for mip-rna markduplicates.
  • Update to repeat expansion calling
  • Adds possibility to rename arriba fusion report from with sample display name
  • Updates documentation

Tools expansionhunter 3.1.2 -> 4.0.2 stranger 0.5.5 -> 0.7

[9.1.2]

  • Increase markduplicates java memory allocation for chromosome 2.
  • Turn off chromograph_viz for wes analysis
  • Chromograph exits gracefully on empty infile
  • Use median coverage instead of expected coverage when evaluating whether expected coverage has been reached or not #1719
  • Fixes infile error in rtg_vcfeval recipe

Tools chromograph 1.0.0 -> 1.0.1

[9.1.1]

  • Fix MIP's gender estaimation for wgs samples with gender set to unknown.

[9.1.0]

  • PNGs generated by chromograph are now uniform in dpi and image size
  • Adds chromograph recipe to generate images of rhocall viz output (regions of autozygosity and fraction of homozygous snps)

Tools chromograph 0.3.3 -> 1.0.0

[9.0.6]

  • Use "PAN" key for slurm_jobs_ids file instead of "ALL" as "ALL" has a size constraint

[9.0.5]

  • Predicted gender from wgs samples are now used in the generated fam files.
  • Restrict plink analysis to intersected target capture kits for mixed wgs/wes cases
  • Update to chromograph in order to fix the renderering coverage images

Tools chromograph: 0.3.1 -> 0.3.3

[9.0.4]

  • Increased memory allocation for samtools_subsample_mt
  • Check that vep plugin paths exists prior to executing mip
  • Cd into cadd temp directory before executing cadd in order to escape snakemake lock errors

[9.0.3]

  • Changed path and name of slurm job ids file to facilitate analysis monitoring
  • SpliceAI annotation with VEP instead of vcfanno
  • Files from Chromograph are no longer compressed into a tarball
  • Sample specific naming of outfiles from rhocall viz
  • Use temporary contig directory for CADD indel calling in order to avoid race condition

Tools chromograph: 0.1.3 -> 0.3.1

[9.0.2]

References

  • clinvar_20200728 -> clinvar_20200905

[9.0.1]

  • Use sample_id in smncopynumber caller instead of file_name_prefix

[9.0.0]

  • Moved annotationof CADD and SPIDEX to vcfanno´s toml config
  • Removed CADD and SPIDEX annotations from Rankvariants recipe, CLI and parameters
  • Turned off bcftools_mpileup by default
  • Replaced sambamba sort with samtools sort after alignment
  • Replaced recipe picartools_mergesamfiles with samtools_merge
  • Replaced sambamba flagstat with samtools flagstat in markduplicates recipe
  • Rename frequency_annotation to variant_annotation
  • Removed option to run sambamba markduplicates for markduplicates recipe
  • Added SpliceAI annotation
  • Collect and evaluate QC metrics generated in the RNA pipeline
  • Per default MIP now installs all programs needed for the different pipelines into one conda environment
  • Add picardtools CollectRnaSeqMetrics to the RNA pipeline
  • Call CYP2D6 alleles with star_caller from the Cyrius package
  • Added bwa_mem2 as an alignemnt option instead of bwa_mem
  • Added option "genomicsdb-shared-posixfs-optimizations" to gatk_genomicsDB to turn off file lock
  • Moved smncopynumbercaller from sample level to case level
  • Added telomerecat analysis for estimating telomere length from wgs

Tools

  • Arriba: 1.1.0 -> 1.2.0
  • bcftools: 1.9=ha228f0b_4 -> 1.10.2-hd2cd319_0 (DNA)
  • bwa-mem2: 2.0-he513fc3_0
  • CADD: v1.5 -> v1.6
  • Cyrius: 1.0
  • expansionhunter: 3.1.2 -> 3.2.2
  • fastqc: 0.11.8-0 -> 0.11.9
  • gatk: 4.1.3.0 -> 4.1.8.1
  • htslib: 1.9-hc238db4_4 -> 1.10.2=h78d89cc_0 (DNA)
  • picard: 2.20.7 -> 2.22.4
  • samtools: 1.9=h8571acd_11 -> 1.10-h9402c20_2 (DNA)
  • SMNCopyNumberCaller: 4b2c1ad -> 1.0
  • STAR 2.7.3a -> 2.7.4a
  • STAR-Fusion v1.8.0 -> v1.9.0
  • stringtie 2.0.3 -> 2.1.3b
  • VEP: 97 -> 100

References

  • clinvar_20191013 -> clinvar_20200728
  • dbNSFP4.0b2a.zip -> dbNSFP4.1a.zip
  • delly_exclude grch37 20150227 -> 20200310
  • grch37_frequency_vcfanno_filter_config_-v1.3-.toml -> grch37_vcfanno_config_-v1.10-.toml
  • grch37_gencode_annotation_-v31-.gtf.gz -> grch37_gencode_annotation_-v34-.gtf.gz
  • grch37_gencode_v19_ctat_lib_plug-n-play_-oct012019-.tar.gz -> grch37_gencode_v19_ctat_lib_plug-n-play_-apr032020-.tar.gz
  • grch37_loqusdb_snv_indel_-2019-11-04-.vcf.gz -> grch37_loqusdb_snv_indel_-2020-03-24-.vcf.gz
  • grch37_loqusdb_sv_-2020-04-20.vcf
  • grch38_frequency_vcfanno_filter_config_-v1.2-.toml -> grch38_frequency_vcfanno_filter_config_-v1.3-.toml
  • grch38_gencode_annotation_-v31-.gtf.gz -> grch38_gencode_annotation_-v34-.gtf.gz
  • grch38_gencode_v31_ctat_lib_plug-n-play_-oct012019-.tar.gz -> grch38_gencode_v31_ctat_lib_plug-n-play_-apr062020-.tar.gz
  • VEP cache: 97 -> 100

[8.2.6]

  • Updates multiqc

Tools

  • multiqc: 1.7 -> 1.9

[8.2.5]

  • Adds output files to store for gatk_combinevariants, sambamba depth, chromograph recipes
  • Use MIPs bcftools singularity image in the conda env when checking references

[8.2.4]

  • Chromograph patch

[8.2.3]

  • Chromograph now creates ideograms over the chromosomes
  • Proband chromograph files are named with sample id instead of case id
  • Increases java memory for picardtools markduplicates

[8.2.2]

  • Fixes a crash in MIP caused by not looping over the Y chromosomes for females in the GATK SplitNCigarReads recipe

[8.2.1]

  • Removes multiple identical entries in the store file. Keeps the most recent

[8.2.0]

  • Minor changes to the install processes
  • Added yamllint
  • New store format file in new file: _deliverables.yaml
  • Fixed memory error in version_collect due to GATK version command
  • Internal code refactoring
  • Updated docs for code style and best practise

Tools

  • ucsc-wigToBigWig: 357
  • ucsc-bedToBigBed: 357

[8.1.0]

  • STAR aligns sample fastq files with the same sequnece mode (eg. single-end or paired-end) within one job
  • Dropped option to run sambamba markduplicates for RNA
  • Added SMNCopyNumberCaller to MIP for SMN calling with WGS data
  • Added downlod of vcf2cytosure blacklist file for grch37

CLI

  • New CLI option for picard markduplicates optical duplicate distance. Default: 2500
  • Removed sambamba markduplicates CLI options from RNA
  • Removed CLI optono markduplicates_no_bam_to_cram
  • New analysis recipe option for smncopynumbercaller
  • New option for vcf2cytosure "--vcf2cytosure_blacklist"

Tools

  • Arriba: 1.1.0
  • SMNCopyNumberCaller: 4b2c1ad
  • vcf2cytosure: 0.4.3 -> 0.5.1

[8.0.0]

  • Added BAM contigs set to allow for single ladies to get a proper check sex (no pun intended:). Actually it is for all female only analyses.
  • Add new recipe to get executable version dynamically and in separate file
  • Remove Snpeff and snpsift from MIP
  • Add clinvar annotation as vep custom file: CLINVAR_CLNSIG,CLINVAR_CLNVID,CLINVAR_CLNREVSTAT now in CSQ field
  • Move frequency annotations from Snpsift to frequency_annotation recipe
  • Moves frequency annotation to separate recipe
  • Adds upd for trios
  • Adds rhocall viz
  • Adds chromograph for chromosome visualization
  • Moves CNVnator to singularity container
  • Moves Manta to singularity container
  • Moves VEP to singularity container
  • Moves Svdb to singularity container and update version to 2.2.0
  • Moves delly to singularity container
  • Moved dbNSFP processing from snpsift to VEP as plugin: GERP++_NR,GERP++_RS,REVEL_rankscore,phastCons100way_vertebrate,phyloP100way_vertebrate is now part of VEP CSQ Schema instead of separate keys in the VCF INFO field
  • Install CADD via MIPs installer
  • Moves STAR to singularity container
  • Moves STAR-Fusion to singularity container
  • Moves RSeQC to singularity container
  • Moves Trim Galore to singularity container
  • Removes the py3 and perl5 conda environment for the RNA pipeline
  • Moves stringtie to singularity container
  • Removed cramtools
  • Removes cutadapt
  • Supply wgs variantcalls for ASE analysis

New references

  • grch37_sv_frequency_vcfanno_filter_config_-v1.2-.toml
  • grch37_frequency_vcfanno_filter_config_-v1.3-.toml

Reference

  • clinvar: 20191013
  • gnomad: r2.0.1 -> r2.1.1
  • loqusdb: 2018-12-18 -> 2019-11-04
  • expansionhunter: 3.0.0 -> 3.1.2

Tools

  • bedtools: 2.27.1-he941832_2 -> 2.29.0=h6ed99ea_1
  • chromograph:
  • expansionhunter: 3.0.0 -> 3.1.2
  • GATK: 4.1.2.0-1 -> 4.1.3.0-0
  • gffcompare: 0.10.6 -> 0.11.2
  • manta: 1.5.0-py27_0 -> 1.6.0-py27_0
  • multiqc: 1.6 -> 1.7
  • picard: 2.18.14-0 -> 2.20.7-0
  • rseqc: 3.0.0 -> 3.0.1
  • rhocall: 0.4 -> 0.5.1
  • rtg-tools: 3.9.1-1 -> 3.10.1-0
  • star: 2.6.1d -> 2.7.3a
  • star-fusion: 1.5.0 -> 1.7.0
  • stranger: 0.5.4 -> 0.5.5
  • stringtie: 1.3.4 -> 2.0.3
  • svdb: 2.0.0 -> 2.2.0
  • trim-galore: 0.5.0 -> 0.6.4
  • upd: 0.1
  • vcfanno: 0.3.1-0 -> 0.3.2-0
  • VEP: 95 -> 97

[7.1.12]

  • Remove upper case in reference file name from test data

[7.1.11]

  • Fixed bug that will casue select vcf files for snv/indel to not be produced if you turn off all SV programs

[7.1.10]

  • Added BAM contigs set to allow for single ladies to get a proper check sex (no pun intended:). Actually it is for all female only analyses.

[7.1.9]

  • Remove race condition between expansionhunter and sambamba depth when reading index files

[7.1.8]

  • Remove MT contig also for analysis run with analysis_type "mixed"

[7.1.7]

  • Use MQ annotation when running GATK VariantRecalibration for SNV

[7.1.6]

  • Use correct recipe name for qccollect path when adding to qc_sample_info.yaml

[7.1.5]

  • Increased sv_varianteffectpredictor memory parameter 9 -> 18 Gb

[7.1.4]

  • Fix bug in outfile_path when mitochondria contig is not part of gene panel

[7.1.3]

  • Increased sv_varianteffectpredictor memory parameter 8 -> 9 Gb

[7.1.2]

  • Update samtools_subsample_mt to fix bug in downsampling of MT bam

[7.1.1]

  • Fixed bug when skipping evaluation in QC_collect

[7.1.0]

  • Updated TIDDIT to enable faster processing
  • Updated GATK for faster haplotypecalling

Tools

  • TIDDIT: 2.5.0 -> 2.7.1
  • bcftools: 1.9-h4da6232_0 -> 1.9=ha228f0b_4
  • bioconductor-deseq2: 1.18.1=r3.4.1_1 -> 1.22.1=r351hf484d3e_0
  • bioconductor-tximport: 1.8.0=r341_0 -> 1.12.0=r351_0
  • GATK: 4.1.0.0-0 -> 4.1.2.0-1
  • samtools: 1.9-h8ee4bcc_1 -> 1.9=h8571acd_11

[7.0.10]

  • option: tiddit_bin_size -> tiddit_coverage_bin_size
  • Added generation of wig coverage data file using tiddit_coverage
  • Added set_recipe_resource options for setting core_number, time, memory on CLI per recipe(s)

New recipes Rd_dna

  • tiddit_coverage

[7.0.9]

  • Removed plink memory allocation from rd_dna_vcf_rerun

[7.0.8]

  • Increased memory allocation for vep (snv/indel) again

[7.0.7]

  • Increased memory allocation for vep (snv/indel)

[7.0.6]

  • Allow "unknown" sex when using expansionhunter by then not using gender in expansionhunter CLI

[7.0.5]

  • Updated stranger to version 0.5.4 to avoid repeat id warnings

Tools

  • stranger: 0.5.1 -> 0.5.4

[7.0.4]

  • Increased recipe memory for plink and vcf2cytosure

[7.0.3]

  • Added removal of genomicsDB dir from potential previous analysis as it causes gatk genotyping to crash

[7.0.2]

  • New framework structure with sub commands - for analysis, install and download
  • New pipelines: rd_dna (previous MIP), rd_dna_vcf_rerun (light rerun from rd_dna data) and rd_rna
  • Install now has sbatch features
  • Download is now only sbatch
  • Added initiation_maps for pipeline engines
  • Changed family to case
  • Changed output data dir structure to flat for each ID
  • Removed call type value in file names
  • Rename module time and cores to recipe time and core
  • Renamed option start_with_program to start_with_recipe
  • Removed use of "p" before recipe names
  • Add check for recipe when using start_with_flag
  • Modify parsing of pedigree to allow new RNA DE keys Fix #554
  • Two-step model for reruns. Fix #546
  • Add input SV vcf for rd_dna_vcf_rerun to qc_sample_info. Fix #548
  • Added io to all recipes
  • Updated GATK to version 4.1.0 for most GATK recipes
  • Removed bed_cov and corresponding R scripts from rare disease analysis
  • Removed bamcalibrationblock and variantannotation block
  • Removed "--rio" option
  • Refactored and updated Delly to "0.7.8". Removed small-indel calling for better speed.
  • Use "--use-best-n-alleles" in freebayes and added default of "4"
  • Add Expansion Hunter Fix #442
  • One case one Multiqc report Fix #515
  • Added exclude contig option. Fix #509.
  • Add UCSC genomicsSuperDups to annotation and rank model. Fix #574
  • Switched to using conda instead of source with conda e.g. "conda activate [ENV]" instead of "source activate [ENV]"
  • Changed default for gatk_calculategenotypeposteriors to 0 (=no).
  • Switched 1000G phase3_v4_2013-05-02 to gnomad r2.0.1 as default for gatk_calculategenotypeposteriors_support_set option
  • Added switch to add all research variants to clinical file for MT. Required to display all MT variants in Scout clinical view as they are all deemed clinically relevant.
  • Added gatk GatherBqsrReports to gather bqsr reports after parallelization
  • Renamed flag "gatk_calculategenotypeposteriors_support_set" to "gatk_calculate_genotype_call_set"
  • Added recipe_memory parameter to parameter definitions and all recipes

New Pipeline

  • rd_dna
  • rd_dna_vcf_rerun
  • rd_rna

New recipes Rd_dna

  • cadd_ar
  • sv_annotate

rd_dna_vcf_rerun

  • sv_vcf_rerun_reformat
  • vcf_rerun_reformat

Annotations

  • genomic_superdups_frac_match
  • REVEL_rankscore
  • CADD for indels
  • MaxEntScan

References

  • clinvar: 20180429 -> 20190305
  • dbnsfp: v2.9 -> v3.5a (GRCh37)
  • GRCh37_gatk_merged_reference_samples.txt
  • GRCh37_mip_sv_svdb_export_-2018-10-09-.vcf
  • VEPs cache: 91 -> 94
  • GRCh37_loqusdb_-2017-05-22-.vcf.gz -> GRCh37_loqusdb_snv_indel_-2018-12-18-.vcf.gz
  • rank_model: 1.21 -> 1.24
  • svrank_model: 1.3 -> 1.8
  • qc_regexp: 1.19 -> 1.22

Tools

  • bcftools: 1.6 -> 1.9-h4da6232_0
  • bedtools: 2.26.0 -> 2.27.1-he941832_2
  • bwa: 0.7.15 -> 0.7.17-ha92aebf_3
  • cadd: 1.4
  • bwakit: 0.7.12 -> 0.7.15-1
  • cutadapt: 1.14 -> 1.18-py27_0
  • cramtools: 3.0.b47 -> 3.0.b127-2
  • expansionhunter: 3.0.0
  • delly: 0.7.7 ->0.8.1-h4037b6b_00
  • fastqc: 0.11.4 -> 0.11.8-0
  • freebayes: 1.1.0 -> 1.2.0-py27h82df9c4_3
  • genmod: 3.7.2 -> 3.7.3
  • GATK: 3.8 -> 4.1.0.0-0 (and some modules still use 3.8)
  • htslib: 1.6 -> 1.9-hc238db4_4
  • manta: 1.1.0 -> 1.5.0-py27_0
  • multiqc: 1.4 -> 1.6
  • peddy: 0.3.1 -> 0.4.2-py_0
  • picardtools: 2.14.1 -> 2.18.14-0
  • rtg-tools: 3.8.4-0 -> 3.9.1-1
  • sambamba: 0.6.6 -> 0.6.8-h682856c_0
  • samtools: 1.6 -> 1.9-h8ee4bcc_1
  • stranger: 0.5.1
  • svdb: 1.1.2 -> 1.3.0-py27h7eb728f_0
  • tiddit: 2.2.5 -> 2.5.0
  • vcf2cytosure: 0.3.0 -> 0.4.3
  • vcfanno: 0.1.0 -> 0.3.1-0
  • vep: 91 -> 94.4

[6.0.7]

  • Increased ploidy when calling variants in the mitochondria. Fix #507
  • New option: 'start_with_program'
  • Fixed chdir inconsistency. Fix #402
  • Added boolean option to qccollect to evaluate plink_gender check with -epg.
  • Moved vcfcytosure processing to the last sv module

[6.0.0]

  • Version 6.0.0. #186