Recent changes to qSignature

qSignature modified by Ollie Holmes

Ollie Holmes — Thu, 04 Aug 2016 06:16:47 -0000

--- v8
+++ v9
@@ -40,7 +40,7 @@
 qsignature modes are invoked by directly naming the class that is to be executed as can be seen in the example below:

 ~~~~
-java -jar qsignature-0.1pre.jar org.qcmg.sig.SignatureGenerator -i <input> -o <output>
+java -cp qsignature-0.1pre.jar org.qcmg.sig.SignatureGenerator -i <input> -o <output>
 ~~~~

 Mode | Description

qSignature modified by John Pearson

John Pearson — Wed, 14 Jan 2015 04:04:37 -0000

--- v7
+++ v8
@@ -45,5 +45,5 @@

 Mode | Description
 -----| -----------
-[SignatureGenerator](/p/adamajava/wiki/qSignature SignatureGenerator) | Generates a vcf file (.qsig.vcf) for a BAM or snp chip file
-[SignatureCompareRelatedSimple](/p/adamajava/wiki/qSignature SignatureCompareRelatedSimple) | Compares all of the qsig.vcf files in a specified folder to ascertain whether there is a potential mixup
+[SignatureGenerator](/p/adamajava/wiki/qSignature SignatureGenerator) | Generates a compressed VCF file (.qsig.vcf.gz) for a BAM or snp chip file
+[SignatureCompareRelatedSimple](/p/adamajava/wiki/qSignature SignatureCompareRelatedSimple) | Compares all of the qsig.vcf.gz files in a specified folder to ascertain whether there is a potential mixup

qSignature modified by John Pearson

John Pearson — Mon, 05 Jan 2015 01:54:36 -0000

--- v6
+++ v7
@@ -7,7 +7,7 @@
 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](http://samtools.github.io/hts-specs/VCFv4.1.pdf). 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 qsignature mode 1 VCF files to calculate the qsignature distance between those samples.
+ * 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 modified by John Pearson

John Pearson — Mon, 05 Jan 2015 01:52:11 -0000

--- v5
+++ v6
@@ -2,9 +2,12 @@
 #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 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: the first mode converts a genotyping array file or a BAM file into a summary file which is based on the Variant Call Format [VCF](http://samtools.github.io/hts-specs/VCFv4.1.pdf). This file summarizes the intensity- or read-based SNP data for a given sample. The second mode performs a pairwise comparison between two VCFs in order to calculate the qsignature distance between those samples. 
+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](http://samtools.github.io/hts-specs/VCFv4.1.pdf). 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 qsignature mode 1 VCF files to calculate the qsignature distance between those samples.

 #Installation#

qSignature modified by Ollie Holmes

Ollie Holmes — Thu, 03 Jul 2014 01:45:08 -0000

--- v4
+++ v5
@@ -4,7 +4,7 @@

 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: the first mode converts a genotyping array file or a BAM file into a summary file which is based on the Variant Call Format [VCF](http://samtools.github.io/hts-specs/VCFv4.1.pdf). This file summarizes the intensity- or read-based SNP data for a given sample. The second mode performs a pairwise comparison between two VCFs in order to calculate the qSignature distance between those samples. 
+qsignature functions in two modes: the first mode converts a genotyping array file or a BAM file into a summary file which is based on the Variant Call Format [VCF](http://samtools.github.io/hts-specs/VCFv4.1.pdf). This file summarizes the intensity- or read-based SNP data for a given sample. The second mode performs a pairwise comparison between two VCFs in order to calculate the qsignature distance between those samples. 

 #Installation#
@@ -18,18 +18,15 @@

 ~~~~
 [oholmes@minion0 qsignature]$ tar xjvf qsignature.tar.bz2
-x antlr-3.2.jar
 x commons-math3-3.1.1.jar
-x ini4j-0.5.2-SNAPSHOT.jar
 x jopt-simple-3.2.jar
 x picard-1.110.jar
-x qbamfilter-1.0pre.jar
 x qcommon-0.1pre.jar
 x qio-0.1pre.jar
-x qmaths-0.1pre.jar
 x qpicard-0.1pre.jar
-x qsnp-1.0.jar
 x sam-1.110.jar
+x Illumina_arrays_design.txt
+x qsignature_positions.txt
 [oholmes@minion0 qsignature]$
 ~~~~

qSignature modified by Ollie Holmes

Ollie Holmes — Tue, 01 Jul 2014 05:03:45 -0000

--- v3
+++ v4
@@ -1,9 +1,10 @@
 [TOC]
 #Introduction#

-qsignature is a tool that is designed to identify sample mixups. It does this by first creating a signature file ([VCF](http://samtools.github.io/hts-specs/VCFv4.1.pdf)) from a BAM file or a snp array file based on around 1.4 million positions in the genome that have been specifically selected.
-It then compares these signature files to try and determine if they belong together.
-The result of the comparison between two qsignature vcf files is a number, and whether or not this number is larger that a specified cutoff indicates a mismatch.
+
+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: the first mode converts a genotyping array file or a BAM file into a summary file which is based on the Variant Call Format [VCF](http://samtools.github.io/hts-specs/VCFv4.1.pdf). This file summarizes the intensity- or read-based SNP data for a given sample. The second mode performs a pairwise comparison between two VCFs in order to calculate the qSignature distance between those samples. 

 #Installation#

qSignature modified by Ollie Holmes

Ollie Holmes — Thu, 19 Jun 2014 06:09:02 -0000

--- v2
+++ v3
@@ -36,4 +36,13 @@
 #Usage#

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

+~~~~
+java -jar qsignature-0.1pre.jar org.qcmg.sig.SignatureGenerator -i  -o 
+~~~~
+
+Mode | Description
+-----| -----------
+[SignatureGenerator](/p/adamajava/wiki/qSignature SignatureGenerator) | Generates a vcf file (.qsig.vcf) for a BAM or snp chip file
+[SignatureCompareRelatedSimple](/p/adamajava/wiki/qSignature SignatureCompareRelatedSimple) | Compares all of the qsig.vcf files in a specified folder to ascertain whether there is a potential mixup

qSignature modified by Ollie Holmes

Ollie Holmes — Thu, 19 Jun 2014 05:56:02 -0000

--- v1
+++ v2
@@ -1,7 +1,7 @@
 [TOC]
 #Introduction#

-qsignature is a tool that is designed to identify sample mixups. It does this by first creating a signature file (VCF) from a BAM file or a snp array file based on around 1.4 million positions in the genome that have been specifically selected.
+qsignature is a tool that is designed to identify sample mixups. It does this by first creating a signature file ([VCF](http://samtools.github.io/hts-specs/VCFv4.1.pdf)) from a BAM file or a snp array file based on around 1.4 million positions in the genome that have been specifically selected.
 It then compares these signature files to try and determine if they belong together.
 The result of the comparison between two qsignature vcf files is a number, and whether or not this number is larger that a specified cutoff indicates a mismatch.

@@ -34,3 +34,6 @@

 #Usage#
+
+
+

qSignature modified by Ollie Holmes

Ollie Holmes — Thu, 19 Jun 2014 05:46:57 -0000

Introduction
Installation
Usage

Introduction

qsignature is a tool that is designed to identify sample mixups. It does this by first creating a signature file (VCF) from a BAM file or a snp array file based on around 1.4 million positions in the genome that have been specifically selected.
It then compares these signature files to try and determine if they belong together.
The result of the comparison between two qsignature vcf files is a number, and whether or not this number is larger that a specified cutoff indicates a mismatch.

Installation

qsignature requires java 7.

Download the qsignature tar file
Untar the tar file into a directory of your choice

You should see jar files for qsignature and its dependencies:

[oholmes@minion0 qsignature]$ tar xjvf qsignature.tar.bz2
x antlr-3.2.jar
x commons-math3-3.1.1.jar
x ini4j-0.5.2-SNAPSHOT.jar
x jopt-simple-3.2.jar
x picard-1.110.jar
x qbamfilter-1.0pre.jar
x qcommon-0.1pre.jar
x qio-0.1pre.jar
x qmaths-0.1pre.jar
x qpicard-0.1pre.jar
x qsnp-1.0.jar
x sam-1.110.jar
[oholmes@minion0 qsignature]$