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Recommended generateNonTrioVariantReport Command

generateNonTrioVariantReport takes as input ATAV output files and generates an excel spreadsheet with a summary table, and nonTrio filtered variants split into separate sheets.

/nfs/goldstein/software/Bioinformatics_Tools/generateVariantReportDragen/generateNonTrioVariantReportDragen\
 -c <ATAV_genotypes.csv> --pt <ATAV_parent_genotypes.csv> -o <output_nonTrio_variant_report.xlsx>

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

-c CSV, --csv=CSV
Input csv from ATAV output file [default = nonTrio/nonTrio_genotypes.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]
-f FILTER, --filter=FILTER
Number of control alleles allowed by the filter [default = 5]
--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 summary table and filtered variants please see Filtering Rules