eggd_vep_helios_config

This repo contains a JSON configuration file for the implementation of VEP for the TSO500 assay.

What does the JSON config do?

Configuration file required to annotate a vcf using Variant Effect Predictor implementation eggd_vep.

A variable level of annotation can be achieved by different combinations of custom annotations and vep plugins, in addition to the required VEP resources.

What does the JSON config version contain?

This json file provides information about annotations,plugins, required fields and the genome version.

• Genome build: GRCh37
• VEP required files:
  • vep_v105.0.tar.gz
  • homo_sapiens_refseq_vep_105_GRCh37.tar.gz
  • Homo_sapiens.GRCh37.dna.toplevel.fa.gz
  • Homo_sapiens.GRCh37.dna.toplevel.fa.gz.fai
  • Homo_sapiens.GRCh37.dna.toplevel.fa.gz.gzi
  • hs37d5.fasta-index.tar.gz
• Custom Annotation sources:
  • clinvar_20241015_GRCh37.vcf.gz
  • gnomad.genomes.r2.0.1.sites.noVEP_normalised_decomposed_PASS.vcf.gz
  • gnomad.exomes.r2.0.2.sites.noVEP_normalised_decomposed_PASS.vcf.gz
• Plugin annotations:
  • REVEL (version May 2022)
    • revel_b37.tsv.gz
  • CADD (v1.6)
    • cadd_whole_genome_SNVs_GRCh37.tsv.gz
    • gnomad.genomes.r2.1.1.indel.tsv.gz
    • InDels_GRCh37.tsv.gz
  • SpliceAI
    • spliceai_scores.masked.snv.hg19.vcf.gz
    • spliceai_scores.masked.indel.hg19.vcf.gz

Notes

How to check the names of all the files included in the config:

config_file=you_file_name.json

# Get the Vep Resources filenames
for file in  $(jq -r ' .vep_resources | .[]' $config_file);
do dx describe $file --json | jq -r '.name';
done

# Get Custom Annotation filenames
for file in  $(jq -r ' .custom_annotations[]|.resource_files[]|.file_id' $config_file);
do dx describe $file --json | jq -r '.name';
done

# Get Plugin Annotation filenames
for file in  $(jq -r ' .plugins[]|.resource_files[]|.file_id' $config_file);
do dx describe $file --json | jq -r '.name';
done