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