GitHub - Fei-Lu/FastCall: Super fast variant caller for whole genome shotgun (WGS) sequencing data (original) (raw)

This project has migrated to (https://github.com/PlantGeneticsLab/TIGER).

Overview

Super fast variant caller for whole genome shotgun (WGS) sequencing data. It works for species with disomic inheritance, including both inbreds and outcrossers.

Prerequisites

Java 8

http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html

Samtools

http://samtools.sourceforge.net/

Usage

From linux command line: java -Xmx200g -jar FastCall.jar parameter.txt > log.txt &

The parameter file is in the released java package. More details of usage are in the parameter file.

Contributor

Fei Lu

flu@genetics.ac.cn; dr.lufei@gmail.com

https://sites.google.com/site/feilu0000/

http://plantgeneticslab.weebly.com/

Citation

Punna Ramu, Williams Esuma, Robert Kawuki, Ismail Y Rabbi, Chiedozie Egesi, Jessen V Bredeson, Rebecca S Bart, Janu Verma, Edward S Buckler, Fei Lu. (2017). Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics. doi: 10.1038/ng.3845!