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