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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Getting the number of support reads for each CNV #250

Open dr-ashu-geno opened 2 years ago

dr-ashu-geno commented 2 years ago

Dear @abyzov

Thank you so much for developing CNVnator.

I used it to call CNVs in all my samples and the program runs successfully until the step for calling CNVs; however, I cannot get the read support for CNVs using -pe option. The program keeps throwing segmentation error similar to the one reported in issue #245. In README page it is written that after running the command for getting the support read, > is shown on the command line and a CNV call should be entered in this format:

chr10:1-10000 del

What if I want to get the number of support reads for all CNVs of all samples by submitting the jobs in SGE system using a shell script and giving the CNV call file as input file without being obliged to enter CNVs one by one? Could you please kindly help me with the full command for getting the read support for each CNV?

Thank you in advance,

Best regards

abyzov commented 2 years ago

Hello, for -pe command you can provide input file with CNVnator calls using -f option

./cnvnator -pe file1.bam ... -qual val(20) -over val(0.8) [-f file]

Alternatively, you can use piping. See section “Additional notes” in the README on GitHub.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, 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