atav.sh --list-mgi --variant PATH_TO_YOUR_VARIANT_FILE --out PATH_TO_OUTPUT_DIR
--list-mgi: trigger list mgi function.
--variant: use a variant id file (one id per line) or a variant id list (comma delimited)
id format: chr-pos-ref-alt
- Variant ID
- Gene Name
- MGI Phenotypes: it lists distinct 'high-level' mouse phenotypes reported for a HGNC gene name, with multiple entries separated using ATAV standards. To serve as a reference.
- MGI Essential: it is a 0/1 indicator to highlight whether that ATAV gene has been linked to lethality when disrupted in mice. To serve as an enrichment reference.
- MGI Seizure: it is a 0/1 indicator to highlight whether that ATAV gene has been linked to seizures when disrupted in mice. To serve as an enrichment reference.
For additional details, please check MGI