Mismatches between the paternal and maternal chromosomes

Q:
I believe I have discovered numerous errors in the NA12878 dataset. We are working with the most recent version,
NA12878_diploid_genome_may3_2011. They are all single base pair mismatches between the paternal and maternal chromosomes in regions that the accompanying .map file marks as contigs.

A:
.map file shows continuous equivalent (without gaps) blocks between haplotypes. BUT THEY DO INCLUDE SNPs. So, heterozygous SNPs will result in base mismatch within a block.

Using CNVnator

Q:
CNVnator is a very popular software as observed though there is no official guide on CNVnator or any directions available on how to get started with CNVnator.Could you be kind enough to provide me with the same, please? Does your license allow to provide commercial services based on your program?

A:
Please download the software and read README file.

Alex Abyzov

Information in .root file

Q:
By using CNVnator, I managed to create the .root file but from there I can’t go any further because when I try to create the histograms, it seem to be working, but it never creates any files after it’s done.
A:
New information is added to the .root file you provided in the command line.
During next calculation step CNVnator will extract this information from the file.

To browse the content of the .root file you can start ROOT and open browser (type “new TBrowser”).

Please see http://root.cern.ch for details.

CNVnator license

Q:
Does your license allow to provide commercial services based on your program?

A:
Commercial services can use CNVnator for free provided that original software/developers/paper is credited/cited.

Alex Abyzov

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Department of Molecular Biophysics and Biochemistry,
Yale University, 260 Whitney ave., P.O. Box 208114,
New Haven, CT, 06520, USA
Phone: 1-(203)-432-5405
e-mail: abyzov@gersteinlab.org
URL: http://homes.gersteinlab.org/people/aabyzov
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