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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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the meaning of genotype "./1" #162

Closed SixPlusSeven closed 5 years ago

SixPlusSeven commented 5 years ago

I found that the vcf file output by CNVnator contains the genotype './1', which I have not seen in the GATK results before. What does the './1' mean?

GWHAAEV00000001 4799801 CNVnator_dup_21 T       <DUP>   .       PASS    END=4803500;SVTYPE=DUP;SVLEN=3700;IMPRECISE;natorRD=3.08695;natorP1=0;natorP2=1.20077e-19;natorP3=0.0128775;natorP4=0.00026256;natorQ0=0.00286944       GT:CN   ./1:3
GWHAAEV00000001 5065201 CNVnator_del_22 T       <DEL>   .       PASS    END=5070800;SVTYPE=DEL;SVLEN=-5600;IMPRECISE;natorRD=0.113962;natorP1=2.84594e-11;natorP2=2.29196e-09;natorP3=4.42701e-11;natorP4=0.00666371;natorQ0=0.425532   GT:CN   1/1:0
GWHAAEV00000001 5600701 CNVnator_dup_23 T       <DUP>   .       PASS    END=5607000;SVTYPE=DUP;SVLEN=6300;IMPRECISE;natorRD=2.58689;natorP1=0;natorP2=8.94537e-10;natorP3=0;natorP4=0.000670899;natorQ0=0.164047        GT:CN   ./1:3

Thanks! Alex

abyzov commented 5 years ago

Hi, in this can copy number is too high, so it is ambiguous whether a dup is homozygous or heterozygous.

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

SixPlusSeven commented 5 years ago

Thanks for your answer!