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Recommended generateVariantReport Command

generateVariantReport takes as input ATAV output files and generates an excel spreadsheet with a summary table, and tier 1 and 2 filtered variants split into separate sheets.

/nfs/goldstein/software/Bioinformatics_Tools/generateVariantReportDragen/generateVariantReportDragen -d <ATAV_dnm_denovoandhom.csv>\
 -c <ATAV_chet_comphet.csv> --pt <ATAV_parents_genotypes.csv> --ptm <ATAV_ptm_parental.mosaic.csv> \
--tnt <ATAV_trioNonTrio_genotypes.csv> -o <output_variant_report.xlsx> 

Required options (will revert to default if not provided):

-c CMPHET, --cmphet=CMPHET
Compound Heterozygous ATAV output file [default = CHET/CHET_comphet.csv]
-d DNM, --dnm=DNM
Denovo Mutation ATAV output file [default = DNM/DNM_denovoandhom.csv]
-t TNT, --tnt=TNT
trioNonTrio ATAV output file [default = trioNonTrio/trioNonTrio_genotypes.csv]
--pt=PT
Parent genotypes ATAV output file [default = parent/parent_genotypes.csv]
--ptm=PTM
Parental mosaic ATAV output file [default = ptlMcsm/ptlMcsm_parental.mosaic.csv]
-o OUT, --out=OUT
Report output file [default = variant_report.xlsx]

Additional options:

-s, --summary
Flag to generate individual sample text summaries [default = False]
-p PHENO, --pheno=PHENO
seqDB file containing sample phenotypes [default = NULL]
--noVEP
Flag to resuse existing VEP output files and skip running VEP [default = False]
-h, --help
Show this help message and exit

For details on the output summary table and filtered variants please see Filtering Rules

generateVariantReport will also create an IGV directory with a dnm.IGV.batch script that can be run in IGV to generate trio screenshots of all identified de novo variants. These should be inspected to validate the quality of the de novo call. The IGV batch script must be run from a windows computer with network access to the IGM nfs drives