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List EVS

Command examples:

atav.sh --list-evs --variant PATH_TO_YOUR_VARIANT_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--list-evs: trigger list evs function.

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

id format: chr-pos-ref-alt

--evs-maf: this is the cutoff used for evs ctrls.

--evs-pop {all}: use this option to specify which population should be used for the evsmaf cutoff. (ea, aa or all)

--exclude-evs-qc-failed: exclude all evs qc failed variants.

--min-evs-all-average-coverage: specify a minimum evs all average coverage value.

Output:

evs.csv

  • Variant ID
  • Evs Eur Covered Samples
  • Evs Eur Average Coverage
  • Evs Afr Covered Samples
  • Evs Afr Average Coverage
  • Evs All Covered Samples
  • Evs All Average Coverage
  • Evs Eur Maf
  • Evs Eur Genotype Count
  • Evs Afr Maf
  • Evs Afr Genotype Count
  • Evs All Maf
  • Evs All Genotype Count
  • Evs Filter Status