Dec 12, 2018 TRUFFLE v1.38 beta has been released.
Introduction
TRUFFLE is a software package for IBD segment detection and relationship estimation. It was designed from scratch with ease of use and low computational overhead in mind. TRUFFLE is intended to be widely applicable and augment standard relationship estimation methods.
Features
- Easy to use and very efficient compared to other segment estimation methods.
- p.IBD1/2 estimation, together with locations and sizes of shared IBD segments.
- Support for multi-sample whole-genome VCF files.
- Integrated variant filtering.
Input file
Single multi-sample autosomal VCF file with >30k variants.
Output
truffle.ibd: p.IBD1 and p.IBD2 estimates of relatedness across every pair of a study
truffle.segments: Shared IBD segment locations and lengths.
truffle.segments: Shared IBD segment locations and lengths.
Quickstart
- Download an example VCF file from 1000 genomes, including 47 individuals and 169413 markers, here:
fs-and-po-pairs-from-1000genomes.vcf.gz
- Download the truffle binary found at the download link: truffle-linux-bin-64.tar.gz
-
Obtain IBD1/2 estimates and list of segments for this example file by running the following command:
./truffle --vcf fs-and-po-pairs-from-1000genomes.vcf.gz --segments
Documentation
Documentation for using truffle is available at the following link:
TRUFFLE Documentation
Download
Warning! TRUFFLE is currently in beta testing mode. If you encounter any problems please contact us through the forums or email.
Linux binary (64-bit)
truffle-linux-bin-64.tar.gz (1.1MB)
Windows and macOS versions are not planned for release at the moment.