10.2.1

Removed mitochondrial frequency filtering. #1944

10.2.0

• Introduced the option --start_after_recipe <recipe_name> to start the pipeline after a given recipe

10.1.0

• Only store qc_metrics_deliverables path in file store for downstream parsing

10.0.3

• Removes duplicates from Glnexus output

10.0.2

• Glnexus are used to genotype the gvcf regardless of how many samples that are analysed.
• Resource bump to the MIP RNA recipe fusion_report

10.0.1

• Fix to gene panel regexp
• Use automated build of MIP
• Increased memory allocation for version_collect

Tools

stranger: 0.7.1 -> 0.8.0

10.0.0

• Remove unused recipe split_fastq_file
• Align with the same bwa mem options as used by Broad
  • Fixed number of bases in each batch
  • Use bwa mem instead of run-bwamem for alignment to grch38
• Use Chanjo repos Docker file instead of MIPs
• Removed support to run bcftools_mpileup as a variant caller
• Added perl and MIP docker file and use it in recipes
• Removed PATH check for proxy bins
• Switched to using container manager instead of proxy bins in recipes
• Removed support to run variant_integrity
• Added deepvariant as variant caller and glnexus to merge samples to case vcf

Tools

arriba: v1.2.0 -> v2.1.0
bedtools: 2.29.0 -> 2.30.0
bwa-mem2 2.0 -> 2.2
chanjo: 4.2.0 -> 4.6
chromograph: 1.0.1 -> 1.1
cyrius: v1.0 -> v1.1
deepvariant: 1.1.0
delly: 0.8.1 -> 0.8.7
gatk: v4.1.8.1 -> v4.2.0.0
glnexus: v1.3.1
megafusion: 66a3a80
multiqc: 1.9 -> 1.10.1
pdfmerger: v1.0
picardtools: 2.23.4 -> 2.25.0
preseq: 2.0.3 -> 3.1.2
rseqc: 3.0.1 -> 4.0.0
rtg-tools: 3.10.1 -> 3.12
salmon: 0.12.0 -> 1.4.0
smncopynumbercaller: 4b2c1ad -> v1.1.1
star: 2.7.4a -> 2.7.8a
stranger: 0.7 -> 0.7.1
svdb: 2.2.0 -> 2.4.0--py37h77a2a36_4
tiddit: 2.8.1 -> 2.12.1
upd: 0.1 -> 0.1.1

References

• clinvar_20200905 -> clinvar_20210415
• VEP cache: 100 -> 103.1
• grch37_gencode_v19_ctat_lib_plug-n-play_-apr032020-.tar.gz -> grch37_gencode_v19_CTAT_lib_Mar012021.plug-n-play.tar.gz
• grch38_gencode_v31_ctat_lib_plug-n-play_-apr062020-.tar.gz -> grch38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz
• gencode annotation: v34 -> v37

9.1.3

• Fix memory allocation for mip-rna markduplicates.
• Updates expansion calling recipe
• Adds possibility to rename arriba fusion report from with sample display name
• Updates documentation

Tools
expansionhunter 3.1.2 -> 4.0.2
stranger 0.5.5 -> 0.7

9.1.2

• Sets java memory to 12G for chromosome 2 when running markdupliates (up from 6)
• Turns of chromograph_rhoviz for wes samples.
• Use median coverage instead of mean coverage when evaluating run
• Updates chromograph to version 1.0.1

9.1.1

• Fixes MIP's gender estimation for wgs samples with gender set to unknown.