WheresWalker

WheresWalker is the software pipeline that helps identify regions of homozygosity to assist in experiments that help relate genotype to phenotype in genes with recessive mutations.

Installation

Whereswalker is written in Bash and Perl, it is cross-platform compatible and no compilation is needed. To install, run:

git clone https://github.com/alekseyzimin/WheresWalker

The main executable is whereswalker.sh. Whereswalker also includes as slightly modified for compatibility version of ANNOVAR software.

Usage

whereswalker.sh [arguments]
-m PATH  mutant vcf file MANDATORY
-w PATH  wild type vcf file MANDATORY
-a PATH  annotation gtf file MANDATORY
-g PATH  genome fasta file MANDATORY
-f PATH  GVF file (see https://github.com/The-Sequence-Ontology/Specifications/blob/master/gvf.md) optional
-t FLOAT starting threshold, the program will iterate down from this threshold, until an interval is found: default:4.0
-v       verbose switch
-h       this message

The GVF (Genome Variation Format) file for the organism is used to optionally screen for known mutations, using Ensembl data. The GVF format is described here: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gvf.md. From the link:

ENSEMBL is providing GVF files for their sequence_alteration data sets at:

ftp://ftp.ensembl.org/pub/current_variation/gvf/
Data from NCBI
The dbVar database at NCBI is providing GVF files for their structural variant data at:

ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_assembly/NCBI36/gvf/
ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_assembly/GRCh37/gvf/
ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_assembly/GRCh38/gvf/

WheresWalker expectc VCF format that is produced by freebayes software with column 10 in the following format: GT:DP:AD:RO:QR:AO:QA:GL. The relevant values from column 10 that are used by the pipeline are 4th and 6th (RO and AO).