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List Trio

Command examples:

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

Command options:

--list-trio: trigger list trio function.

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

Note:
The trio defined in sample file has to have one case child and two parents.
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
  • Denovo Flag: de novo, newly homozygous, or possibly/unlikely one of these

comphet.csv

  • Family ID
  • Child
  • Sample Type (Child)
  • Mother
  • Father
  • 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.

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.

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

High Confidence

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

Medium Confidence

POSSIBLY DE NOVO
POSSIBLY DE NOVO; IN REF
POSSIBLY NEWLY HEMIZYGOUS
POSSIBLY NEWLY HEMIZYGOUS; IN REF

Low Confidence

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