Support for hg38 from fastq to ranked variants

[henrikstranneheim]

Recipes

• [x] fastqc
• [x] bwa_mem
• [x] picardtools_mergesamfiles
• [x] markduplicates
• [x] gatk_baserecalibration
• [x] chanjo_sexcheck
• [x] samtools_subsample_mt
• [x] tiddit_coverage
• [x] sambamba_depth (test new exons file: "grch38_scout_exons-2019-09-16-.bed"; Clinical-Genomics/scout#644)
• [x] picardtools_collectmultiplemetrics
• [x] picardtools_collecthsmetrics (curerntly capture kit is used and not scout exons, change? test new exons file: "grch38_scout_exons-2019-09-16-.bed"; Clinical-Genomics/scout#644)
• [x] cnvnator_ar
• [x] expansionhunter 3.0.0 with 3.0.1 var_cat_file
• [x] manta
• [x] tiddit
• [x] delly_call
• [x] delly_reformat
• [x] sv_combinevariantcallsets
• [ ] sv_annotate (works with INFO field reduced gnomad file reset memory to 7Gb) Needs liftover files to grch38:
  • grch37_svdb_query_clingen_cgh_benign_-v1.0.0-.vcf (Daniel: ?)
  • grch37_svdb_query_clingen_cgh_pathogenic_-v1.0.0-.vcf (Daniel: ?)
  • grch37_svdb_query_clingen_ngi_-v1.0.0-.vcf (Daniel: Skip)
  • grch37_mip_sv_svdb_export_-2018-10-09-.vcf (Rerun cases ~200)
  • grch37_swegen_concat_sort_-20170830-.vcf (Available on swefreq)
  • grch37_svdb_query_decipher_-v1.0.0-.vcf (Daniel investigates)
  • grch37_gnomad.genomes_-r2.1.1_sv-.vcf (Daniel: Skip)
• [x] sv_varianteffectpredictor
• [x] sv_vcfparser
• [ ] sv_rankvariant Need update to grch38:
  • grch37_cust003-cmms-red-pen_-2017-.tsv (Clinical-Genomics/scout#1300)
• [x] sv_reformat
• [x] vcf2cytosure_ar (dnil comment below)
• [x] gatk_haplotypecaller (but long runtime 21 h,solved with reduced gnomad file)
• [ ] gatk_genotypegvcfs Need to reprocess for grch38 (WES)
  • gatk_genotypegvcfs_ref_gvcf: grch37_gatk_merged_reference_samples.txt (Rerun cases ~30-40 WES)
• [x] gatk_gathervcfs
• [x] gatk_variantrecalibration (Works with maxgaussian 6 (case/data dependent; (livingox))
• [x] gatk_combinevariantcallsets
• [x] rtg_vcfeval
• [x] peddy
• [x] plink_ar
• [x] variant_integrity_ar
• [x] gatk_variantevalall
• [x] prepareforvariantannotationblock
• [x] rhocall
• [ ] variant_annotation
  • [x] gnomad
  • [x] swegen
  • [ ] grch38_loqusdb_snv_indel_-XXXX-XX-XX-.vcf.gz (Rerun cases and moonso/loqusdb#65)
  • [ ] grch38_genbank_haplogroup
  • [x] CADD
  • [x] SpliceAI
• [x] frequency_filter
• [x] cadd_ar
• [x] varianteffectpredictor
• [x] vcfparser_ar
• [ ] rankvariant Need update of reduced_penetrance file
  • grch37_cust003-cmms-red-pen_-2017-.tsv (Clinical-Genomics/scout#1300)
• [x] endvariantannotationblock
• [x] gatk_variantevalexome
• [x] qccollect_ar
• [x] multiqc_ar
• [x] analysisrunstatus
• [x] sacct