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eggd_vep_TWE_config

Json configuration file for the implementation of VEP for the TWE 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