qSignature

John Pearson Ollie Holmes

Introduction

qsignature is a simple and highly effective method for detecting potential sample mix-ups using distance measurements between SNP alleles that are common to pairs of samples of interest. qsignature can use both genotyping array and high-throughput sequencing data to detect potential mix-ups and can be applied across multiple sequencing platforms and experiment types.

qsignature functions in two modes:

  • mode 1 processes a genotyping array file or BAM file to create a summary file in a format based on the Variant Call Format VCF. This file summarizes the intensity- or read-based SNP data for a given sample and only needs to be run once per genotype or BAM file;
  • mode 2 performs a pairwise comparison between two or more qsignature mode 1 VCF files to calculate the qsignature distances between the samples.

Installation

qsignature requires java 7.

You should see jar files for qsignature and its dependencies:

[oholmes@minion0 qsignature]$ tar xjvf qsignature.tar.bz2
x commons-math3-3.1.1.jar
x jopt-simple-3.2.jar
x picard-1.110.jar
x qcommon-0.1pre.jar
x qio-0.1pre.jar
x qpicard-0.1pre.jar
x sam-1.110.jar
x Illumina_arrays_design.txt
x qsignature_positions.txt
[oholmes@minion0 qsignature]$

Usage

qsignature modes are invoked by directly naming the class that is to be executed as can be seen in the example below:

java -cp qsignature-0.1pre.jar org.qcmg.sig.SignatureGenerator -i <input> -o <output>
Mode Description
SignatureGenerator Generates a compressed VCF file (.qsig.vcf.gz) for a BAM or snp chip file
SignatureCompareRelatedSimple Compares all of the qsig.vcf.gz files in a specified folder to ascertain whether there is a potential mixup

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