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@henrikstranneheim henrikstranneheim released this 14 May 08:13
· 4102 commits to master since this release
v7.0.2
3d1f5d6
  • 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
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