List Sibling Comp Het¶
- 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
atav.sh --list-sibling-comp-het --sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR
--list-sibling-comp-het: trigger list sibling compound heterozygosity function.
All the Command Options are available to use in this function.
- Family ID
"Shared" or "Possibly Shared" or "Not Shared"
- Child1 Trio Comp Het Flag
- Child2 Trio Comp Het Flag
Please check Output Columns for common columns.
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|