GRCh38 reference

[tstokowy]

Hi, I would like to use CNVnator to analyze samples aligned to GRCh38.p10. Is this possible?

-- Tomasz Stokowy Senior Engineer Department of Clinical Science University of Bergen, Norway

[abyzov]

Hi, yes it is possible. Info about the ref genome is parsed from bam header.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

[rmf4]

I was checking cnvnator.cpp and Genome.cpp and I can not find where GRCh38 (hg38) is applied. Moreover in the usage help code seems hg38 is not listed. Is there some piece of code that CNVnator treat this issue?

[abyzov]

Hi, the information about the reference genome used for alignment is parsed from bam header. So, no need to worry that there is genome description in the source code. Specifying genome in command line is also not necessary.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

[astulaaa]

Does that also apply to older versions? Specifically asking about v0.3.3

Thanks, Asta

[abyzov]

Yes.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745