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List Trio Denovo

Command examples:

atav.sh --list-trio-denovo --sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--list-trio-denovo: trigger list trio denovo function.

--run-tier: trigger to run tier1 & tier2 scripts at the end.

All the Command Options are available to use in this function.

Note: the calculation of variant frequency in control includes all control parents except the parents of affected child.

Output:

denovoandhom.csv

  • Family ID
  • Child: ID of the offspring
  • Mother: ID of the mother
  • Father: ID of the father
  • Flag: de novo, newly homozygous, or possibly/unlikely one of these

Please check Output Columns for common columns.

For a further analysis, please check Trio_Analysis_Framework.