Difference between revisions of "Contra"
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{{Bioinformatics application | {{Bioinformatics application | ||
− | |sw summary=Copy number analysis for exome-sequencing / targeted-resequencing. Two methods of analysis available: Case vs Control, or Case vs Baseline. Function available for creating a baseline from multiple samples | + | |sw summary=Copy number analysis for exome-sequencing / targeted-resequencing. Two methods of analysis available: Case vs Control, or Case vs Baseline. Function available for creating a baseline from multiple samples. |
− | |bio domain= | + | |bio domain=Sequencing, Cancer biology, Genomics, Copy number estimation, |
− | |||
|bio tech=Illumina | |bio tech=Illumina | ||
|created by=Jason Li | |created by=Jason Li | ||
|created at=Peter MacCallum Cancer Centre, East Melbourne VIC 3002, Australia | |created at=Peter MacCallum Cancer Centre, East Melbourne VIC 3002, Australia | ||
|maintained=Yes | |maintained=Yes | ||
− | |input format=BAM, BED, | + | |input format=BAM, BED, |
− | |output format=VCF, Tab-delimited, | + | |output format=VCF, Tab-delimited, |
|sw feature=Copy number analysis, baseline (pseudo-control) creation | |sw feature=Copy number analysis, baseline (pseudo-control) creation | ||
|language=Python, R | |language=Python, R | ||
|library=BEDtools, SAMtools | |library=BEDtools, SAMtools | ||
− | |licence= | + | |licence=GPLv3, |
− | |os=Linux 64, Linux, | + | |os=Linux 64, Linux, |
}} | }} | ||
== Description == | == Description == |
Latest revision as of 00:07, 20 December 2015
Application data |
|
Created by | Jason Li |
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Biological application domain(s) | Sequencing, Cancer biology, Genomics, Copy number estimation |
Technology | Illumina |
Created at | Peter MacCallum Cancer Centre, East Melbourne VIC 3002, Australia |
Maintained? | Yes |
Input format(s) | BAM, BED |
Output format(s) | VCF, Tab-delimited |
Software features | Copy number analysis, baseline (pseudo-control) creation |
Programming language(s) | Python, R |
Software libraries | BEDtools, SAMtools |
Licence | GPLv3 |
Operating system(s) | Linux 64, Linux |
Summary: Copy number analysis for exome-sequencing / targeted-resequencing. Two methods of analysis available: Case vs Control, or Case vs Baseline. Function available for creating a baseline from multiple samples.
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Description
CONTRA implements a method for CNV detection for targeted resequencing data, including whole-exome capture data. It calls copy number gains and losses for each target region based on normalized depth of coverage. Key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation.
See publication:
Li, et al. Bioinformatics (2012) 28 (10): 1307-1313. FULL TEXT HERE
Links
References
none specified
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