D3b RADIANT Annotation

Simple workflow to reannotate Kids First VEPs to be compatible with the RADIANT framework. However, this can also be used to annotate/reannotate any other VCF as needed to ensure the following requirements are met:

Old annotations are stripped
VCF is normalized
VCF is annotated with VEP
Exomiser is run

Tools Run

bcftools strip: Uses annotate to remove existing VEP (CSQ) and gnomad 3.1.1 (gnomad_3_1_1*) annotations
bcftools norm: Uses norm to split (or join) mulit-allelics and normalize indels

VEP: Uses cache 111 and meets the following specific criteria:

--canonical
--format vcf 
--hgvs 
--hgvsg 
--no_stats 
--numbers 
--offline 
--fields Allele,Consequence,IMPACT,SYMBOL,Feature_type,Gene,PICK,Feature,EXON,BIOTYPE,INTRON,HGVSc,HGVSp,STRAND,CDS_position,cDNA_position,Protein_position,Amino_acids,Codons,VARIANT_CLASS,HGVSg,CANONICAL,RefSeq,MANE,MANE_SELECT,MANE_PLUS 
--flag_pick 
--mane 
--mane_select 
--pick_order rank,biotype,mane_select,mane_plus_clinical,canonical,appris,tsl,ccds,length,ensembl,refseq 
--symbol 
--variant_class 
--vcf 
--xref_refseq 
--compress_output bgzip
--fasta Homo_sapiens_assembly38.fasta
--assembly GRCh38
--species homo_sapiens
--cache
--cache_version 111

exomiser: "The Exomiser is a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data." See https://github.com/exomiser/Exomiser for more details

Inputs

What is "required" or not depends upon the input. The Required inputs are based on Kids First Processed VCFs. You may use the disable_(insert_step) flags to skip any step not needed based on the input.

Required - Need to provide

vcf: KF VCF to process
vcf_index = Index of vcf
output_basename: String prefix of file outputs. Technically optional, but strongly recommended. Default is TEST

VEP

vep_cache: VEP cache for annotation. Recommend 111, homo_sapiens_vep_111_GRCh38.tar.gz
fasta: FASTA used during variant calling. Recommend Homo_sapiens_assembly38.fasta

EXOMISER

analysis_file: YAML with analysis options. See https://exomiser.readthedocs.io/en/latest/advanced_analysis.html#analysis. Recommend default_exomiser_WGS_analysis.yml

datadir_file: TAR GZ with referenece files. Example contents:

data/
data/remm/
data/remm/ReMM.v0.4.hg38.tsv.gz.tbi
data/remm/ReMM.v0.4.hg38.tsv.gz
data/2406_hg38.sha256
data/2406_hg38/
data/2406_hg38/2406_hg38_transcripts_refseq.ser
data/2406_hg38/2406_hg38_transcripts_ensembl.ser
data/2406_hg38/2406_hg38_genome.mv.db
data/2406_hg38/2406_hg38_variants.mv.db
data/2406_hg38/2406_hg38_transcripts_ucsc.ser
data/2406_hg38/2406_hg38_clinvar.mv.db
data/cadd/
data/cadd/1.7/
data/cadd/1.7/whole_genome_SNVs.tsv.gz
data/cadd/1.7/whole_genome_SNVs.tsv.gz.tbi
data/cadd/1.7/gnomad.genomes.r4.0.indel.tsv.gz
data/cadd/1.7/gnomad.genomes.r4.0.indel.tsv.gz.tbi
data/2406_phenotype/
data/2406_phenotype/2406_phenotype.mv.db
data/2406_phenotype/rw_string_10.mv
data/2406_phenotype/phenix/
data/2406_phenotype/phenix/out/
data/2406_phenotype/phenix/out/10.out
data/2406_phenotype/phenix/out/9_symmetric.out
data/2406_phenotype/phenix/out/14.out
data/2406_phenotype/phenix/out/13_symmetric.out
data/2406_phenotype/phenix/out/20.out
data/2406_phenotype/phenix/out/19.out
data/2406_phenotype/phenix/out/16_symmetric.out
data/2406_phenotype/phenix/out/7.out
data/2406_phenotype/phenix/out/3_symmetric.out
data/2406_phenotype/phenix/out/8.out
data/2406_phenotype/phenix/out/17_symmetric.out
data/2406_phenotype/phenix/out/15_symmetric.out
data/2406_phenotype/phenix/out/5_symmetric.out
data/2406_phenotype/phenix/out/11.out
data/2406_phenotype/phenix/out/14_symmetric.out
data/2406_phenotype/phenix/out/8_symmetric.out
data/2406_phenotype/phenix/out/10_symmetric.out
data/2406_phenotype/phenix/out/1.out
data/2406_phenotype/phenix/out/20_symmetric.out
data/2406_phenotype/phenix/out/11_symmetric.out
data/2406_phenotype/phenix/out/18_symmetric.out
data/2406_phenotype/phenix/out/4.out
data/2406_phenotype/phenix/out/19_symmetric.out
data/2406_phenotype/phenix/out/2.out
data/2406_phenotype/phenix/out/12.out
data/2406_phenotype/phenix/out/15.out
data/2406_phenotype/phenix/out/2_symmetric.out
data/2406_phenotype/phenix/out/9.out
data/2406_phenotype/phenix/out/17.out
data/2406_phenotype/phenix/out/16.out
data/2406_phenotype/phenix/out/6_symmetric.out
data/2406_phenotype/phenix/out/13.out
data/2406_phenotype/phenix/out/18.out
data/2406_phenotype/phenix/out/3.out
data/2406_phenotype/phenix/out/4_symmetric.out
data/2406_phenotype/phenix/out/1_symmetric.out
data/2406_phenotype/phenix/out/7_symmetric.out
data/2406_phenotype/phenix/out/6.out
data/2406_phenotype/phenix/out/5.out
data/2406_phenotype/phenix/out/12_symmetric.out
data/2406_phenotype/phenix/hp.obo
data/2406_phenotype/phenix/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt
data/2406_phenotype/hp.obo

pheno_file: YAML file with sample information

Individual example:

  ---
  id: FM_ZCF17CPC
  proband:
  subject:
      id: BS_4JPDCXVR
      sex: MALE
  phenotypicFeatures:
      - type:
          id: HP:0009733
          label: Glioma
  pedigree:
  persons:
      - individualId: BS_4JPDCXVR
      sex: MALE
      affectedStatus: AFFECTED

  metaData:
  resources:
      - id: hp
      name: human phenotype ontology
      url: http://purl.obolibrary.org/obo/hp.owl
      version: hp/releases/2019-11-08
      namespacePrefix: HP
      iriPrefix: 'http://purl.obolibrary.org/obo/HP_'
  phenopacketSchemaVersion: 2.0

Family example:

 ---
 id: FM_ASMHHE2N
 proband:
 subject:
     id: BS_KPAR4N94
     sex: MALE
 phenotypicFeatures:
     - type:
         id: HP:0009733
 pedigree:
 persons:
     - individualId: BS_KPAR4N94
     sex: MALE
     paternalId: BS_264QQD38
     maternalId: BS_EQ98CJJT
     affectedStatus: AFFECTED
     - individualId: BS_264QQD38
     sex: MALE
     affectedStatus: UNAFFECTED
     - individualId: BS_EQ98CJJT
     sex: FEMALE
     affectedStatus: UNAFFECTED
 metaData:
 resources:
     - id: hp
     name: human phenotype ontology
     url: http://purl.obolibrary.org/obo/hp.owl
     version: hp/releases/2019-11-08
     namespacePrefix: HP
     iriPrefix: 'http://purl.obolibrary.org/obo/HP_'
 phenopacketSchemaVersion: 2.0

Required - Has defaults

BCFTOOLS

rm_fields_csv: List of existing annotation to remove. Default:

  INFO/CSQ,INFO/gnomad_3_1_1_AC,INFO/gnomad_3_1_1_AN,INFO/gnomad_3_1_1_AF,INFO/gnomad_3_1_1_nhomalt,INFO/gnomad_3_1_1_AC_popmax,INFO/gnomad_3_1_1_AN_popmax,INFO/gnomad_3_1_1_AF_popmax,INFO/gnomad_3_1_1_nhomalt_popmax,INFO/gnomad_3_1_1_AC_controls_and_biobanks,INFO/gnomad_3_1_1_AN_controls_and_biobanks,INFO/gnomad_3_1_1_AF_controls_and_biobanks,INFO/gnomad_3_1_1_AF_non_cancer,INFO/gnomad_3_1_1_primate_ai_score,INFO/gnomad_3_1_1_splice_ai_consequence,INFO/gnomad_3_1_1_FILTER,INFO/gnomad_3_1_1_AF_non_cancer_afr,INFO/gnomad_3_1_1_AF_non_cancer_ami,INFO/gnomad_3_1_1_AF_non_cancer_asj,INFO/gnomad_3_1_1_AF_non_cancer_eas,INFO/gnomad_3_1_1_AF_non_cancer_fin,INFO/gnomad_3_1_1_AF_non_cancer_mid,INFO/gnomad_3_1_1_AF_non_cancer_nfe,INFO/gnomad_3_1_1_AF_non_cancer_oth,INFO/gnomad_3_1_1_AF_non_cancer_raw,INFO/gnomad_3_1_1_AF_non_cancer_sas,INFO/gnomad_3_1_1_AF_non_cancer_amr,INFO/gnomad_3_1_1_AF_non_cancer_popmax,INFO/gnomad_3_1_1_AF_non_cancer_all_popmax

VEP

assembly: GRCh38
vep_cache_version: 111
vep_species: homo_sapiens
vep_cpus: 32

EXOMISER

datadir_name: data
cadd_indelname: gnomad.genomes.r4.0.indel.tsv.gz
cadd_snvname: whole_genome_SNVs.tsv.gz
cadd_version: 1.7
exomiser_version: 2406
exomiser_genome: hg38
exomiser_mem: 16
remm_filename: ReMM.v0.4.hg38.tsv.gz
remm_version: v0.4

Optional

BCFTOOLS STRIP

annotate_vcf: VCF to use to add annotations using bcftools
annotate_vcf_index: Index of annotate_vcf
annot_fields_csv: CSV list of fields to use from annotate_vcf and/or list of fields to rename
bcftools_strip_extra_args: Extra args to add to the step. Consult tool manual if needed

BCFTOOLS NORM

check_ref: For BCFTOOLS norm. Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites. Default is w
multiallelics: Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any. Default is -any

VEP

vep_buffer_size: 100000

EXOMISER

local_frequency: custom frequency source file
local_frequency_index: Index of local_frequency

Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
.github		.github
conf		conf
docs/logo		docs/logo
modules/local		modules/local
test_inputs		test_inputs
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
main.nf		main.nf
nextflow.config		nextflow.config
nextflow_schema.json		nextflow_schema.json
sb_nextflow_schema.yaml		sb_nextflow_schema.yaml

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D3b RADIANT Annotation

Tools Run

Inputs

Required - Need to provide

VEP

EXOMISER

Required - Has defaults

BCFTOOLS

VEP

EXOMISER

Optional

BCFTOOLS STRIP

BCFTOOLS NORM

VEP

EXOMISER

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D3b RADIANT Annotation

Tools Run

Inputs

Required - Need to provide

VEP

EXOMISER

Required - Has defaults

BCFTOOLS

VEP

EXOMISER

Optional

BCFTOOLS STRIP

BCFTOOLS NORM

VEP

EXOMISER

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