atav.sh --list-trio--sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR
--list-trio: trigger list trio function.
All the Command Options are available to use in this function.
The calculation of variant frequency in control includes all control parents except the parents of affected child.
- Family ID
- Child: ID of the offspring
- Mother: ID of the mother
- Father: ID of the father
- Denovo Flag: de novo, newly homozygous, or possibly/unlikely one of these
- Family ID
- Sample Type (Child)
- Comp Het 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.
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.
denovo with inherited variant rules:
|De Novo\Inherited Variant||High Confidence||Low Confidence|
|High Confidence||denovo with inherited variant||possibly denovo with inherited variant|
|Medium Confidence||possibly denovo with inherited variant||no flag|
|Low Confidence||possibly denovo with inherited variant||no flag|
DE NOVO DE NOVO; IN REF NEWLY HEMIZYGOUS NEWLY HEMIZYGOUS OR POSSIBLY DE NOVO NEWLY HEMIZYGOUS OR POSSIBLY DE NOVO; IN REF NEWLY HEMIZYGOUS; IN REF
POSSIBLY DE NOVO POSSIBLY DE NOVO; IN REF POSSIBLY NEWLY HEMIZYGOUS POSSIBLY NEWLY HEMIZYGOUS; IN REF
UNLIKELY DE NOVO UNLIKELY DE NOVO OR NEWLY HEMIZYGOUS UNLIKELY DE NOVO OR NEWLY HEMIZYGOUS; IN REF UNLIKELY DE NOVO; IN REF UNLIKELY NEWLY HEMIZYGOUS UNLIKELY NEWLY HEMIZYGOUS; IN REF
For a further analysis, please check Diagnostic Analysis Framework