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Family Analysis

Command examples:

atav.sh --family-analysis --family-id PATH_TO_FAMILY_ID_FILE --sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--family-analysis: trigger family analysis function.

--family-id: specify either a single family id or a family id file, which contains one family id per line. (family id is the first column defined in your sample file)

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

Note: recessive rules - family hom case > 0 & family het case = 0 & family ref case = 0

Output:

shared.csv and notshare.csv:

Please check Output Columns for common columns.

summary.only.shared.csv and summary.all.shared.csv

  • Gene Name
  • RVIS ALL_0.1%MAF Percentile
  • RVIS OEratio Percentile
  • RVIS EdgeCase
  • Artifacts in Gene
  • Total Shared Variant Family
  • Total Shared Het Family
  • Total Shared Hom Family
  • Total Shared Cpht Family
  • Total SNV
  • Total Indel
  • Family IDs
  • Variant IDs

Note: Flag column - Shared, Different zygosity, Possibly shared and Not shared.

Shared: if all of the cases are hom or all the cases are het.
Different zygosity: if all the cases are either hom or het (but not all hom and not all het).
Partially shared: in a family with more than 2 cases, 2 or more cases have the variant but some cases in the family either do not have the variant or are missing.
Possibly shared: if all of the cases are either hom, het, or missing
Not shared: if only some cases are hom or het, and the others are not missing