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List gnomAD Genome

Command examples:

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

Command options:

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

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

Output:

gnomad.genome.csv

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