MendelianCheck.md

MendelianCheck

This command writes a report on the prevalence of Mendelian errors in the given data set.

General considerations

Files need to be formatted as detailed here.

The tested allele is selected as detailed here.

Mendelian error prevalence is estimated as detailed here.

Command line

java -Xmx16G -cp your/folder/triogen-X.Y.Z/triogen-X.Y.Z.jar no.uib.triogen.cmd.mendelian_check.MendelianCheck [parameters]

Note: you need to replace your/folder by the folder where the release is installed, and Z.Y.Z by the version number.

Standard parameters

-h/--help                 Display help text
-v/--version              Display version

Mandatory Parameters

-g/--geno                 The genotypes file.
-c/--chromosome           The name of the chromosome (1-22, X/23, or Y/24 - please keep the naming of sex chromosome consistent across all files)
-f/--fam                  The trio identifiers file.
-o/--out                  The file where to write the results.

Additional Parameters

-vi/--variantId           File listing the variants to include in the analysis. Default: process all variants in the genotypes file.
-af/--afThreshold         Allele frequency threshold. 0.005 excludes all alleles of variants with frequency < 0.5% or > 99.5%. Default: 0.005.
-nv/--nVariants           The number of variants to process in parallel. Default is the number of cores on the machine.
-z/--timeOut              The number of days before timeout, default is 365.

Processing

For each variant, the number of tested alleles for each haplotype is counted and compared to the expected number of alleles based on the allele frequency.

Output

The output is a text file with one line per variant.