Support for hg38 from fastq to ranked variants

[henrikstranneheim]

Recipes

• fastqc
• bwa_mem
• picardtools_mergesamfiles
• markduplicates
• gatk_baserecalibration
• chanjo_sexcheck
• samtools_subsample_mt
• tiddit_coverage
• sambamba_depth (test new exons file: "grch38_scout_exons-2019-09-16-.bed"; Use scout to export Exons for chanjo scout#644)
• picardtools_collectmultiplemetrics
• picardtools_collecthsmetrics (curerntly capture kit is used and not scout exons, change? test new exons file: "grch38_scout_exons-2019-09-16-.bed"; Use scout to export Exons for chanjo scout#644)
• cnvnator_ar
• expansionhunter 3.0.0 with 3.0.1 var_cat_file
• manta
• tiddit
• delly_call
• delly_reformat
• 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)
• sv_varianteffectpredictor
• sv_vcfparser
• sv_rankvariant
  Need update to grch38:
  • grch37_cust003-cmms-red-pen_-2017-.tsv (Export of reduced penetrance file based on gene panels via CLI scout#1300)
• sv_reformat
• vcf2cytosure_ar (dnil comment below)
• 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)
• gatk_gathervcfs
• gatk_variantrecalibration (Works with maxgaussian 6 (case/data dependent; (livingox))
• gatk_combinevariantcallsets
• rtg_vcfeval
• peddy
• plink_ar
• variant_integrity_ar
• gatk_variantevalall
• prepareforvariantannotationblock
• rhocall
• variant_annotation
  • gnomad
  • swegen
  • grch38_loqusdb_snv_indel_-XXXX-XX-XX-.vcf.gz (Rerun cases and Lift MAF snp profile to grch38 loqusdb#65)
  • grch38_genbank_haplogroup
  • CADD
  • SpliceAI
• frequency_filter
• cadd_ar
• varianteffectpredictor
• vcfparser_ar
• rankvariant
  Need update of reduced_penetrance file
  • grch37_cust003-cmms-red-pen_-2017-.tsv (Export of reduced penetrance file based on gene panels via CLI scout#1300)
• endvariantannotationblock
• gatk_variantevalexome
• qccollect_ar
• multiqc_ar
• analysisrunstatus
• sacct

[henrikstranneheim]

Done as far as we can go internally with MIP. Will open new issues for dealing with what is left in terms of annotation, building data references and updating rank model.

[dnil]

Native gnomAD hg38 available with their v3! See eg https://twitter.com/LFranciol/status/1184515095029800962
Oh, and I did talk to the person doing the ClinGen array dumps, who says we can get a lift over from the array software, which I assume has a decent lift over of the array oligo positions.

[dnil]

Hm, I was doing some maintenance on vcf2cytosure and realise it should not be marked hg38 ready as of yet. It a) needs a reference CGH def for hg38 and b) has some hard-coded contig sizes etc that need generalising.

[henrikstranneheim]

Noted! Let me kow when you are ready.

[jemten]

@dnil, any updates on that vcf2cytosure file?

[dnil]

@dnil, any updates on that vcf2cytosure file?

Right, no, but I'll pass the ping on and hopefully be back soon with news!