7.1.9

• Fix possible race condition between expansionhunter and sambamba depth

7.1.8

• Limit mixed case to wes contigs

7.1.7

• Use MQ annotation when running GATK VariantRecalibration for SNV

7.1.6

• Added correct recipe name to qc_sample_info.yaml

7.1.5

• Increased sv_varianteffectpredictor memory parameter 9 -> 18 Gb

7.1.4

• Fixed bug with outfile path when mitochondria contig is not part of gene panel

v7.1.3

[7.1.3]

• Increased sv_varianteffectpredictor memory parameter 8 -> 9 Gb

v7.1.2

[7.1.2]

• Update samtools_subsample_mt to fix bug in downsampling of MT bam
• Fixed bug when skipping evaluation in QC_collect

v7.1.0

[7.1.0]

• Updated TIDDIT to enable faster processing
• Updated GATK for faster haplotypecalling
• Removed plink memory allocation from rd_dna_vcf_rerun
• Increased memory allocation for vep (snv/indel)
• Allow "unknown" sex when using expansionhunter by then not using gender in expansionhunter CLI
• Updated stranger to version 0.5.4 to avoid repeat id warnings
• Increased recipe memory for plink and vcf2cytosure
• Added removal of genomicsDB dir from potential previous analysis as it causes gatk genotyping to crash

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
• stranger: 0.5.1 -> 0.5.4

v7.0.2

• 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