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List MGI

Command examples:

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

Command options:

--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

Output:

mgi.csv

  • 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