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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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GT:CN ./1:inf #283

Open jingydz opened 1 year ago

jingydz commented 1 year ago

Hi, in some samples, I get the variation record is "chrM 1 CNVnator_dup_1 N . PASS END=17000;SVTYPE=DUP;SVLEN=17000;IMPRECISE;natorRD=inf;natorP1=0;natorP2=0;natorP3=0;natorP4=0;natorQ0=0.00908054 GT:CN ./1:inf". When I use the bcftools software to merge, I get the error: [W::vcf_parse_format] Extreme FORMAT/CN value encountered and set to missing at chrM:1 [E::vcf_parse_format] Invalid character 'i' in 'CN' FORMAT field at chrM:1

I wonder why the copy number is inf?

abyzov commented 1 year ago

Hi, do you have the original line in CNVnator format for this records? Having this line would facilitate understanding of what is happening.

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 7-91 Rochester, MN 55905 www.abyzovlab.org http://www.abyzovlab.orgtel: +1-(507)-538-0978