eggd_vep_CEN_config

Json configuration file for the implementation of VEP for the CEN assay.

What does this 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 annotation , vep plugins in addition to the required VEP resources.

What does this config version contain?

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

• Genome build: GRCh37
• VEP required files:
  • vep_v107.0.tar.gz
  • plugin_config.txt
  • homo_sapiens_refseq_vep_107_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.r2.1.1.sites.all.noVEP_normalised_decomposed_PASS.dias_trimmed_v1.0.0.vcf.bgz
  • gnomad.exomes.r2.1.1.sites.noVEP_normalised_decomposed_PASS.dias_trimmed_v1.0.0.vcf.bgz
  • TWE_POPAF_N500_chr1-22_220413.vcf.gz
  • HGMD_Pro_2024.3_hg19.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