Skip to content

Latest commit

 

History

History
103 lines (94 loc) · 4.15 KB

CHANGELOG.md

File metadata and controls

103 lines (94 loc) · 4.15 KB

Change Log

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

[7.0.0]

  • 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
  • Added initiation_maps for pipeline engine
  • 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 Clinical-Genomics#554
  • Two-step model for reruns. Fix Clinical-Genomics#546
  • Add input SV vcf for rd_dna_vcf_rerun to qc_sample_info. Fix Clinical-Genomics#548
  • Added io to all recipes
  • Updated GATK to version 4.0.11 for most GATK recipes
  • Removed bed_cov and corresponding R scripts from rare disease analysis
  • Removed variantannotation block - "--rio" now only operates on BAM block
  • 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 Clinical-Genomics#442
  • One case one Multiqc report Fix Clinical-Genomics#515
  • Added exclude contig option. Fix Clinical-Genomics#509.
  • Add UCSC genomicsSuperDups to annoation and rank model. Fix Clinical-Genomics#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

New Pipeline

  • rd_dna
  • rd_dna_vcf_rerun

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 -> 20181028
  • 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 -> 1.23
  • svrank_model: 1.3 -> 1.5
  • qc_regexp: 1.19 -> 1.20

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: 2.5.5
  • delly: 0.7.7 -> 0.7.8-h278814d_3
  • 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 -> 1.4.0-py27_1
  • 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: 0.4
  • 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 Clinical-Genomics#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]