eggd_vep_CENCNV_config

Json configuration file for CEN assay CNV variant annotation using VEP.

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:
  • None for CNV analysis at the moment.

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