mrCaNaVaR (mɪstər ʤʌnʌvʌr) is a copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.

2013-09-04: mrCaNaVaR version 0.51 release:

  • Minor bug in CW counting is fixed.

2013-07-02: mrCaNaVaR version 0.5 release:

  • SAM files can now separately be read into *.depth files, and then merged.
  • New -nsam parameter to read specific SAM files in the READ mode.
  • New CONC mode (--conc) to concatenate/merge different *.depth files using the new -concdepth parameter. These different files may be from different library preparations (see below).
  • Multiple library support added.
  • Several bug fixes.

2012-11-26: mrCaNaVaR version 0.41 release:

  • Bugs in non-autosomal chromosome processing for male samples are fixed.

2012-09-23: mrCaNaVaR version 0.4 release:

  • Pseudoautosomal support added through -pseudoa paramater. You can enter the pseudoautosomal regions in BED format in the PREP mode. This is optional; but the configuration file generated and used by this version is not compatible with the previous versions. You need to recreate the configuration file using the PREP mode.
  • Code cleanup to facilitate easier addition of new features.

2012-06-01: mrCaNaVaR version 0.35 release:

  • SAM headers are now ignored.

2011-12-07: mrCaNaVaR version 0.34 release:

  • Segmentation fault with some kernels & gcc due to an unallocated string is fixed.
2011-10-17: mrCaNaVaR version 0.33 release:
  • Compilation errors in MacOSX are fixed.
  • Compilation error in x86_64 systems with gcc version > 4.33 is fixed.

2011-08-15: mrCaNaVaR version 0.32 release:

  • Minor bug in parsing chromosome names that end with whitespace is fixed.

2011-06-22: mrCaNaVaR version 0.31 release:

  • Bug causing infinite loop in control region selection is fixed..

2011-04-16: mrCaNaVaR version 0.3 release:

  • Bug in GC normalization is fixed.
  • Bug in CN estimation in chrX and chrY for male mammals is fixed.

2011-03-04: mrCaNaVaR version 0.22 release:

  • GC counting bug in LW when an assembly gap is 1 character is fixed.

2011-03-02: mrCaNaVaR version 0.21 release:

  • Bug causing segmentation fault when CW_SIZE is set to a small value is fixed.

2011-02-25: mrCaNaVaR version 0.2 release:

  • A bug in GC normalization is fixed.

2011-01-28: mrCaNaVaR version 0.1 release:

  • Initial release of mrCaNaVaR.
  • This version only predicts absolute copy numbers. CNV interval output will be included in the next release. For the time being, you can select intervals with increased copy number (i.e. > 2.5) and merge such intervals using BEDtools.

Latest Releases

Related Projects

mrFAST: Our default Illumina read mapper that finds both indels and mismatches and performs iterative search to increase mapping sensitivity. Specifically designed for copy number variation and structural variation analysis.

mrsFAST: Our alternative Illumina read mapper that finds only mismatches to increase mapping speed. Also supports bisulfite mapping.

drFAST: Read mapper for  di-base color-space reads generated with the SOLiD platform.

NovelSeq: Novel sequence insertion discovery framework.

SCALCE: Tool for compression of FASTQ files.

SPLITREAD: Detection of structural variants and indels from genome and exome sequencing data

VariationHunter: Structural variation calling algorithm using read pairmapping information including suboptimal alignments.


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