8.2.4

Fixes error in directory naming for chromograph and adds subdirectories for chromograph output

8.2.3

Fixes naming of chromograph files and increases java memory for markduplicates

8.2.2

Fixes an issue that caused the the RNA GATK BaseRecalibration recipe to crash

8.2.1

Fixes an issue with duplicate entries in the store file

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 option markduplicates_no_bam_to_cram
• New analysis recipe option for smncopynumbercaller
• New option for vcf2cytosure "--vcf2cytosure_blacklist"

Tools

• vcf2cytosure: 0.4.3 -> 0.5.0
• Arriba: 1.1.0

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

CLI

• Removes the noupdate option from the installation

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 cause 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.