Project

General

Profile

List Trio Compound Het

Command examples:

atav.sh --list-trio-comp-het --sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--list-trio-comp-het: trigger list trio compound het function

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

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

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

Output:

comphet.csv

  • Family ID
  • Child
  • Sample Type (Child)
  • Mother
  • Father
  • Flag
  • Multi qualified var combinations
  • Var Case Freq #1 & #2 (co-occurance)
  • Var Ctrl Freq #1 & #2 (co-occurance)

Please check Output Columns for common columns.

Note:

The compound heterozygote hypothesis is termed "Shared" if none of the above is true, and the genotype calls support proper inheritance. It is considered "Possibly Shared," or "Possibly Compound Heterozygote" if none of the previous was the case, but there was ambiguity, i.e. that a parent's call was homozygous for the minor allele but the read depth was insufficient to be confident about it.

For further analysis, please check Trio_Analysis_Framework.