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
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.
- Compilation errors in MacOSX are fixed.
- Compilation error in x86_64 systems with gcc version > 4.33
2011-08-15: mrCaNaVaR version 0.32 release:
- Minor bug in parsing chromosome names that end with whitespace
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
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.