Input file formats

Following is a list of input file formats and the report builders they are used in.

Input argument	candidategenereportfile , candidategenefile , or genepanelinfofile
Report builders	Multi-family Mendelian analysis, De novo/CHZ for trios, Sample QC and statistics
Format	This parameter points to the candidate gene file (.tsv, .rep, .gor) which the CSA generates for each study (located in the corresponding study folder under studies in the folder tree); there are four required columns: chrom, gene_start, gene_end, gene_symbol

candidategenereportfile, candidategenefile, or genpanelinfofile

Input argument	candidategenereportgrid
Report builders	Multi-family Mendelian analysis, Mendelian analysis, De novo/CHZ for trios
Format	This is an alternative to candidategenereportfile ; GOR grid in an open tab with four required columns: chrom, gene_start, gene_end, gene_symbol

candidategenereportgrid

Input argument	customAlleleFreqFile
Report builders	Multi-family Mendelian analysis, Mendelian analysis, De novo/CHZ for trios
Format	A GOR variant file with additional columns for alleleFreq and PNcount (the Variant QC and statistics report builder can be used to calculate such allele frequencies); the column containing allele frequencies must be lableled “alleleFreq” and the column containing the number of carriers of the variants must be labeled “PNcount”

customeAlleleFreqFile

Input argument	customAnnotationFile
Report builders	Mendelian analysis, De novo/CHZ for trios
Format	A GOR variant file with annotation columns; maximum one line per variant

customAnnotationFile

Input argument	customRegionFile
Report builders	Mendelian analysis, De novo/CHZ for trios
Format	A GOR region file to add custom annotations such as CNVs (not to filter); file should contain at least three columns (chrom, bpstart, bpstop) as the first three columns (column names do not need to match these terms)

customRegionFile

Input argument	exclusionRegions
Report builders	Variant association
Format	A GOR segment file (containing chrom, bpstart, bpstop columns) that defines regions to be excluded (column names do not need to match these terms)

exclusionRegions

Input argument	exclusionVarfile
Report builders	Gene association, Multi-family Mendelian analysis, Mendelian analysis, De novo/CHZ for trios
Format	A GOR variant file (containing chrom, pos, ref, and alt columns) with variants to be excluded from the analysis (column names do not need to match these terms)

exclusionVarfile

Input argument	genelist
Report builders	Used in many report builders
Format	One single-column grid containing gene symbols; the column name is either gene_symbol or gene

genelist

Input argument	Genepanelinfofile
Report builders	Multi-family Mendelian analysis, Mendelian analysis, De novo/CHZ for trios, Transcripts
Format	A .tsv, .rep, or .gor file with the following columns: gene_symbol, gene_DmaxAf, gene_MOI, gene_RmaxAf, Gene_RmaxGf. This file allows the default RmaxAf, RmaxGf, and DmaxAf to be overwritten per gene symbol. Column names should match the five column names listed, and the gene_symbol column should be the first column.

Genepanelinfofile

Input argument	geneReport
Report builders	Genes to pathways, Genes to paralogs
Format	Data grid contains the gene information; the first column should be the chromosome (the column name is not important), and the second to fourth columns should be start position, end position, and gene symbol (these three columns should be named “gene_start | gene_begin”, “gene_end | gene_stop”, “gene_symbol | gene”)

geneReport

Input argument	gorReport or variantreport
Report builders	Used in many report builders
Format	Data grid contains the variant information; the first two columns should be chromosome and position (the column names are not important), and the third and fourth columns should be named “Ref/reference” and “Call/Allele/Alt” respectively

gorReport or variantreport

Input argument	pedigree
Report builders	De novo/CHZ for trios
Format	Three required columns with the following column names: PN (sample ID of index case), FN (sample ID of father), and MN (sample ID of mother)

pedigree

Input argument	Regionfile
Report builders	Multi-family Mendelian analysis, Mendelian analysis, De novo/CHZ for trios, Sample QC and statistics
Format	A GOR segment file (containing chrom,*bpstart*,*bpstop* columns) that defines regions to be included or excluded (column names do not need to match these terms)

Regionfile

Input argument	rsIDfile
Report builders	Risk SNPs
Format	A grid (.rep) file containing a list of sIDs in a column named “rsids”

rsIDfile

Input argument	rsIDgrid
Report builders	Risk SNPs
Format	An open grid containing a list of rsIDs in a column named “rsids”

rsIDgrid

Input argument	Sample ID grid
Input names in many report builders	CASEs, CTRLs, subjects
Format	One-column grid contains PN only (can be any column name)

Sample ID grid

Input argument	SubjectAnnotation
Report builders	Gene association, Gene analysis
Format	Adds columns to output from an open grid which has a column of subject IDs and associated columns (e.g., subject phenotypes); the first column should contain PNs (subject/sample IDs), and the column should be named “PN”

SubjectAnnotation