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List gnomAD Exome

Command examples:

atav.sh --list-gnomad-exome --variant PATH_TO_YOUR_VARIANT_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--list-gnomad-exome: trigger list gnomad-exome function.

--variant: use a variant id file (one id per line) or a variant id list (comma delimited)

id format: chr-pos-ref-alt

--region: use a region file or a region list (comma delimited)

region format: chr:start-end

--gnomad-exome-pop is to specify which population (global, controls, non_neuro, afr, amr, asj, eas, sas, fin, nfe, controls_afr, controls_amr, controls_asj, controls_eas, controls_sas, controls_fin, controls_nfe, non_neuro_afr, non_neuro_amr, non_neuro_asj, non_neuro_eas, non_neuro_sas, non_neuro_fin, non_neuro_nfe) should be used for the gnomad-exome maf cutoff. you can require the cutoff to be met in multiple populations by putting a comma between them, for example --gnomad-exome-pop afr,amr,nfe.

--gnomad-exome-af is to specify a threshold and it will require variants to pass the threshold in all populations from --gnomad-exome-pop

Output:

gnomad.exome.csv

  • Variant ID
  • gnomAD Exome FILTER
  • gnomAD Exome segdup
  • gnomAD Exome lcr
  • gnomAD Exome decoy
  • gnomAD Exome rf_tp_probability
  • gnomAD Exome qd
  • gnomAD Exome pab_max
  • gnomAD Exome global_AF
  • gnomAD Exome global_AN
  • gnomAD Exome global_nhet
  • gnomAD Exome global_nhomalt
  • gnomAD Exome global_nhemi
  • gnomAD Exome controls_AF
  • gnomAD Exome controls_AN
  • gnomAD Exome controls_nhet
  • gnomAD Exome controls_nhomalt
  • gnomAD Exome controls_nhemi
  • gnomAD Exome non_neuro_AF
  • gnomAD Exome non_neuro_AN
  • gnomAD Exome non_neuro_nhet
  • gnomAD Exome non_neuro_nhomalt
  • gnomAD Exome non_neuro_nhemi
  • gnomAD Exome afr_AF
  • gnomAD Exome amr_AF
  • gnomAD Exome asj_AF
  • gnomAD Exome eas_AF
  • gnomAD Exome sas_AF
  • gnomAD Exome fin_AF
  • gnomAD Exome nfe_AF
  • gnomAD Exome nfemax_AF
  • gnomAD Exome easmax_AF
  • gnomAD Exome controls_afr_AF
  • gnomAD Exome controls_amr_AF
  • gnomAD Exome controls_asj_AF
  • gnomAD Exome controls_eas_AF
  • gnomAD Exome controls_sas_AF
  • gnomAD Exome controls_fin_AF
  • gnomAD Exome controls_nfe_AF
  • gnomAD Exome controls_nfemax_AF
  • gnomAD Exome controls_easmax_AF
  • gnomAD Exome non_neuro_afr_AF
  • gnomAD Exome non_neuro_amr_AF
  • gnomAD Exome non_neuro_asj_AF
  • gnomAD Exome non_neuro_eas_AF
  • gnomAD Exome non_neuro_sas_AF
  • gnomAD Exome non_neuro_fin_AF
  • gnomAD Exome non_neuro_nfe_AF
  • gnomAD Exome non_neuro_nfemax_AF
  • gnomAD Exome non_neuro_easmax_AF