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List Sibling Comp Het

Definition:

  • identify variants shared between the two children (or found in one child but missing in the other child (b/c of coverage cutoff or failing QC threshold))
  • restrict to variants where 2 qualifying variants are found in the same gene
  • restrict to variant combinations where one variant is found in 1 parent and the other variant is found in the other parent.
  • the function is now support to analyze multi affected Children

Command examples:

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

Command options:

--list-sibling-comp-het: trigger list sibling compound heterozygosity function.

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

Output:

comphet.csv

  • Family ID
  • Mother
  • Father
  • Flag

"Shared" or "Possibly Shared" or "Not Shared"

  • Child1
  • Child1 Trio Comp Het Flag
  • Child2
  • Child2 Trio Comp Het Flag

Please check Output Columns for common columns.

Note:

As of October 2015, the List Trio Compound Het rules were updated. The sibling compound het function now uses the output from that function, treating the quad as a pair of trios in the following manner:

Sibling 1 Flag Shared Possibly Shared Not Shared
Sibling 2 Flag
Shared Shared Possibly Shared Not Shared
Possibly Shared Possibly Shared Possibly Shared Not Shared
Not Shared Not Shared Not Shared Not Shared