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-0.14.jar -h
A basic call looks as follows:
# java -jar jped-cli-0.14.jar -m MODE IN.ped IN.vcf 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
of inheritance and the pedigree.
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.