JPed - Filter for Compatible Variants

The Jannovar package de.charite.compbio.jannovar.filter contains functionality to load PED files and check lists of genotype calls for compatibility with a given pedigree and a selected mode of inheritance. This functionality is exposed in the jped-cli program. You can get the command line help for jped-cli as follows:

# java -jar jped-cli-0.16.jar --help

A basic call looks as follows:

# java -jar jped-cli-0.16.jar -m MODE(S) -p IN.ped -i IN.vcf -o OUT.vcf

This call of jped-cli will first read in the pedigree from IN.ped. Then, it will read the file IN.vcf and filter the variants therein for compatibility with the given MODE(S) of inheritance and the pedigree. Multiple MODE(S)` can be used. This can be usefull if you like to have autosomal dominant and x recessive in one file. The resulting VCF file will be written to OUT.vcf.

Available Modes of Inheritance

You can select one of the following modes of inheritance:

AUTOSOMAL_DOMINANT
Require compatibility with autosomal dominant mode of inheritance. This can also be used to filter for de novo mutations.
AUTOSOMAL_RECESSIVE
Require compatibility with autosomal recessive mode of inheritance.
X_RECESSIVE
Require compatibility with X-recessive mode of inheritance.
X_DOMINANT
Require compatibility with X-dominant mode of inheritance.

Gene-Wise Processing

By default, jped-cli checks each record individually for compatibility. Of course, this does not account for composite recessive autosomal mode of inheritance. Here, all variants for a given gene have to be analyzed.

To enable gene-wise processing, you have to pass the --gene-wise flag and pass in a path to a Jannovar database (a .ser file, as previously downloaded with jannovar download). In this case, jped-cli will check all variants for compatibility with the selected mode of inheritance and will write out all variants in genes with possible compatibility.

Note

When doing gene-wise processing, all variants are written out for a gene for which a compatible mutation was found. This sometimes causes confusion for users.