Recent changes to Home

Home modified by John Pearson

John Pearson — Mon, 30 Nov 2015 00:38:09 -0000

--- v26
+++ v27
@@ -1,6 +1,6 @@
 The AdamaJava project holds code for variant callers and pipeline tools related to next-generation sequencing (NGS).  The code was created by members of the Queensland Centre for Medical Genomics ([QCMG](http://www.qcmg.org)) as part of their participation in the International Cancer Genome Consortium ([ICGC](http://www.icgc.org)).  The code is now being developed and maintained by the [Genome Informatics Group](http://www.qimrberghofer.edu.au/lab/genome-informatics/) at the [QIMR Berghofer Medical Research Institute](http://www.qimrberghofer.edu.au).

-While the repository contains code for dozens of utilities, the list below shows tools that are considered robust enough to be released for general use.  Most are written in Java and require version 1.7 or above.  Some tools and helper scripts may be written in other languages, primarily perl and groovy.  Some tools have dependencies on other software.
+While the repository contains code for dozens of utilities, the list below shows tools that are considered robust enough to be released for general use.  Most are written in Java and require version 1.7 although some now require version 1.8 or above.  Some tools and helper scripts may be written in other languages, primarily perl and groovy.  Some tools have dependencies on other software.

 * [qAmplicon](/p/adamajava/wiki/qAmplicon/) - design primer pairs for variant verification
 * [qCnv](/p/adamajava/wiki/qCnv/) - a pre-processor for copy number variant (CNV) calling

Home modified by John Pearson

John Pearson — Mon, 23 Nov 2015 01:15:26 -0000

--- v25
+++ v26
@@ -1,4 +1,4 @@
-The AdamaJava project holds code for variant callers and pipeline tools related to next-generation sequencing (NGS).  The code was created by members of the Queensland Centre for Medical Genomics ([QCMG](http://www.qcmg.org)) as part of their participation in the International Cancer Genome Consortium ([ICGC](http://www.icgc.org)).  The code is now being developed and maintained by the Genome Informatics Group at the [QIMR Berghofer Medical Research Institute](http://www.qimrberghofer.edu.au).
+The AdamaJava project holds code for variant callers and pipeline tools related to next-generation sequencing (NGS).  The code was created by members of the Queensland Centre for Medical Genomics ([QCMG](http://www.qcmg.org)) as part of their participation in the International Cancer Genome Consortium ([ICGC](http://www.icgc.org)).  The code is now being developed and maintained by the [Genome Informatics Group](http://www.qimrberghofer.edu.au/lab/genome-informatics/) at the [QIMR Berghofer Medical Research Institute](http://www.qimrberghofer.edu.au).

 While the repository contains code for dozens of utilities, the list below shows tools that are considered robust enough to be released for general use.  Most are written in Java and require version 1.7 or above.  Some tools and helper scripts may be written in other languages, primarily perl and groovy.  Some tools have dependencies on other software.

Home modified by q.xu

q.xu — Wed, 27 Aug 2014 04:56:19 -0000

--- v24
+++ v25
@@ -13,7 +13,7 @@
 * [qCoverage](/p/adamajava/wiki/qCoverage/) - calculates coverage statistics given a BAM file with mapped reads
 * [qSignature](/p/adamajava/wiki/qSignature/) - a method for detecting potential sample mix-ups using distance measurements between SNP alleles that are common to pairs of samples of interest
 * [qMotif](/p/adamajava/wiki/qMotif/) - search for motifs in a BAM file
-* [qMito](/p/adamajava/wiki/qMito/) - gathers base-level metrics across mitochondria reference from a group of BAMs. output format is tsv.
+

 Some QCMG tools have been released as separate SourceForge Projects

Home modified by q.xu

q.xu — Tue, 26 Aug 2014 06:40:25 -0000

--- v23
+++ v24
@@ -13,6 +13,7 @@
 * [qCoverage](/p/adamajava/wiki/qCoverage/) - calculates coverage statistics given a BAM file with mapped reads
 * [qSignature](/p/adamajava/wiki/qSignature/) - a method for detecting potential sample mix-ups using distance measurements between SNP alleles that are common to pairs of samples of interest
 * [qMotif](/p/adamajava/wiki/qMotif/) - search for motifs in a BAM file
+* [qMito](/p/adamajava/wiki/qMito/) - gathers base-level metrics across mitochondria reference from a group of BAMs. output format is tsv.

 Some QCMG tools have been released as separate SourceForge Projects

Home modified by John Pearson

John Pearson — Tue, 05 Aug 2014 07:40:07 -0000

--- v22
+++ v23
@@ -1,4 +1,4 @@
-The AdamaJava project holds code for variant callers and pipeline tools related to next-generation sequencing (NGS).  The code was created by members of the Queensland Centre for Medical Genomics ([QCMG](http://www.qcmg.org)) as part of their participation in the International Cancer Genome Consortium ([ICGC](http://www.icgc.org)).
+The AdamaJava project holds code for variant callers and pipeline tools related to next-generation sequencing (NGS).  The code was created by members of the Queensland Centre for Medical Genomics ([QCMG](http://www.qcmg.org)) as part of their participation in the International Cancer Genome Consortium ([ICGC](http://www.icgc.org)).  The code is now being developed and maintained by the Genome Informatics Group at the [QIMR Berghofer Medical Research Institute](http://www.qimrberghofer.edu.au).

 While the repository contains code for dozens of utilities, the list below shows tools that are considered robust enough to be released for general use.  Most are written in Java and require version 1.7 or above.  Some tools and helper scripts may be written in other languages, primarily perl and groovy.  Some tools have dependencies on other software.

Home modified by Ollie Holmes

Ollie Holmes — Tue, 08 Jul 2014 05:24:30 -0000

--- v21
+++ v22
@@ -12,6 +12,7 @@
 * [qBamfilter](/p/adamajava/wiki/qBamfilter/) - filters records from a BAM file
 * [qCoverage](/p/adamajava/wiki/qCoverage/) - calculates coverage statistics given a BAM file with mapped reads
 * [qSignature](/p/adamajava/wiki/qSignature/) - a method for detecting potential sample mix-ups using distance measurements between SNP alleles that are common to pairs of samples of interest
+* [qMotif](/p/adamajava/wiki/qMotif/) - search for motifs in a BAM file

 Some QCMG tools have been released as separate SourceForge Projects

Home modified by Ollie Holmes

Ollie Holmes — Thu, 03 Jul 2014 01:27:06 -0000

--- v20
+++ v21
@@ -11,6 +11,7 @@
 * [qPileup](/p/adamajava/wiki/qPileup/) - gathers base-level metrics across a whole genome from a group of BAMs
 * [qBamfilter](/p/adamajava/wiki/qBamfilter/) - filters records from a BAM file
 * [qCoverage](/p/adamajava/wiki/qCoverage/) - calculates coverage statistics given a BAM file with mapped reads
+* [qSignature](/p/adamajava/wiki/qSignature/) - a method for detecting potential sample mix-ups using distance measurements between SNP alleles that are common to pairs of samples of interest

 Some QCMG tools have been released as separate SourceForge Projects

Home modified by Ollie Holmes

Ollie Holmes — Thu, 19 Jun 2014 04:48:14 -0000

--- v19
+++ v20
@@ -8,8 +8,9 @@
 * [qProfiler](/p/adamajava/wiki/qProfiler/) - summary statistics on BAM files for use in QC assessment
 * [qSnp](/p/adamajava/wiki/qSnp/) - heuristics-based tumour/normal single nucleotide variant (SNV) caller 
 * [qSv](/p/adamajava/wiki/qsv/) - tumour/normal structural variant (SV) caller 
-* [qPileup](/p/adamajava/wiki/qPileup/) - gathers base-level metrics across a whole genome from a group of bams
-* [qBamfilter](/p/adamajava/wiki/qBamfilter/) - filters records from a bam file
+* [qPileup](/p/adamajava/wiki/qPileup/) - gathers base-level metrics across a whole genome from a group of BAMs
+* [qBamfilter](/p/adamajava/wiki/qBamfilter/) - filters records from a BAM file
+* [qCoverage](/p/adamajava/wiki/qCoverage/) - calculates coverage statistics given a BAM file with mapped reads

 Some QCMG tools have been released as separate SourceForge Projects

Home modified by John Pearson

John Pearson — Tue, 10 Jun 2014 01:22:51 -0000

--- v18
+++ v19
@@ -1,6 +1,6 @@
 The AdamaJava project holds code for variant callers and pipeline tools related to next-generation sequencing (NGS).  The code was created by members of the Queensland Centre for Medical Genomics ([QCMG](http://www.qcmg.org)) as part of their participation in the International Cancer Genome Consortium ([ICGC](http://www.icgc.org)).

-While the repository contains code for dozens of utilities, the following tools have been released for general use. java 1.7 and above is required and some tools have dependencies on other software.
+While the repository contains code for dozens of utilities, the list below shows tools that are considered robust enough to be released for general use.  Most are written in Java and require version 1.7 or above.  Some tools and helper scripts may be written in other languages, primarily perl and groovy.  Some tools have dependencies on other software.

 * [qAmplicon](/p/adamajava/wiki/qAmplicon/) - design primer pairs for variant verification
 * [qCnv](/p/adamajava/wiki/qCnv/) - a pre-processor for copy number variant (CNV) calling

Home modified by Ollie Holmes

Ollie Holmes — Sun, 25 May 2014 23:38:22 -0000

--- v17
+++ v18
@@ -9,7 +9,7 @@
 * [qSnp](/p/adamajava/wiki/qSnp/) - heuristics-based tumour/normal single nucleotide variant (SNV) caller 
 * [qSv](/p/adamajava/wiki/qsv/) - tumour/normal structural variant (SV) caller 
 * [qPileup](/p/adamajava/wiki/qPileup/) - gathers base-level metrics across a whole genome from a group of bams
-* [qBamfilter](/p/adamajava/wiki/qBamfilter/) --sdfsf
+* [qBamfilter](/p/adamajava/wiki/qBamfilter/) - filters records from a bam file

 Some QCMG tools have been released as separate SourceForge Projects