9.1.0

9.1.0

• PNGs generated by chromograph are now uniform in dpi and image size
• Adds chromograph recipe to generate images of rhocall viz output (regions of autozygosity and fraction of homozygous snps)

Tools
chromograph 0.3.3 -> 1.0.0

9.0.6

• Use "PAN" key for slurm_jobs_ids file instead of "ALL" as "ALL" has a size constraint

9.0.5

• Predicted gender from wgs samples are now used in the generated fam files.
• Restrict plink analysis to intersected target capture kits for mixed wgs/wes cases
• Update to chromograph in order to fix the renderering coverage images

Tools
chromograph 0.3.1 -> 0.3.3

9.0.4

• Increased memory allocation for samtools_subsample_mt
• Check that vep plugin paths exists prior to executing mip
• Cd into cadd temp directory before executing cadd in order to escape snakemake lock errors

9.0.3

• Changed path and name of slurm job ids file to facilitate analysis monitoring
• SpliceAI annotation with VEP instead of vcfanno
• Files from Chromograph are no longer compressed into a tarball
• Sample specific naming of outfiles from rhocall viz
• Use temporary contig directory for CADD indel calling in order to avoid race condition

Tools

• chromograph: 0.1.3 -> 0.3.1

9.0.2

References

• clinvar_20200728 -> clinvar_20200905

9.0.1

• Use sample_id in smncopynumber caller instead of file_name_prefix

9.0.0

• 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

8.2.6

Updates MultiQC to version 1.9

8.2.5

• Adds output files to store for gatk_combinevariants, sambamba depth, chromograph recipes
• Use MIPs bcftools singularity image in the conda env when checking references