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:
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]$
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>
|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|