List Trio Compound Het¶
atav.sh --list-trio-comp-het --sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR
--list-trio-comp-het: trigger list trio compound het function
--run-tier: trigger to run tier1 & tier2 scripts at the end.
All the Command Options are available to use in this function.
- Family ID
- Sample Type (Child)
- 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.
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.