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@henrikstranneheim henrikstranneheim released this 15 Sep 06:53
· 1379 commits to master since this release
v9.0.0
2289d4e
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Learn about vigilant mode.
  • 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
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