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Recommended ATAV Commands

Listed are recommended ATAV commands for trio, non-trio, parental mosaicism transmission, and coverage analyses. Non-trio analysis is run in cases where a full trio was not available, or is run in addition to the standard trio analysis whenever there is evidence for transmission of a clinically relevant genetic variant from similarly or mildly affected parent(s).

All commands require a tab-delimited trio sample file. Sample file format:

FamilyID CHGVID CHGVID CHGVID Gender(1=M,2=F) Status(1=control/parent,2=case/proband) SeqType ExomeSamPrepKit
diagseq12 diagseq25f12 diagseq27f12 diagseq26f12 1 2 Exome Roche
diagseq12 diagseq27f12 0 0 1 1 Exome Roche
diagseq12 diagseq26f12 0 0 2 1 Exome Roche
Control1 Control1 0 0 2 1 Exome 50MB
Control2 Control2 0 0 1 1 Exome 50MB
Control3 Control3 0 0 1 1 Exome Roche
Control4 Control4 0 0 2 1 Exome Roche
Control5 Control5 0 0 1 1 Genome N/A
Control6 Control6 0 0 1 1 Genome N/A

Trio Report ATAV Commands

Non-Trio Report ATAV Command

Coverage ATAV Command