the -1.00 value of CN in SV.sv.vcf file

hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation

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the -1.00 value of CN in SV.sv.vcf file #120

Closed LcQian closed 6 years ago

LcQian commented 6 years ago

Hi, I have no idea of the -1.00 value of CN in SV.sv.vcf file. Can you explain it to me please? Thanks a lot！ Below is an example of my vcf.

1 1420459 2 N . . SVTYPE=DUP;SVLEN=37837;END=1458296;STRANDS=-+:14;IMPRECISE;CIPOS=-269,10;CIEND=-10,323;CIPOS95=-47,3;CIEND95=-1,28;SU=14;PE=14;SR=0 GT:SU:PE:SR:CN ./.:6:6:0:-1.00 ./.:8:8:0:-1.00

ernfrid commented 6 years ago

A value of -1 is returned when CNVnator is unable to determine a copy number. See this issue in the CNVnator repository for more information: https://github.com/abyzovlab/CNVnator/issues/83

LcQian commented 6 years ago

Thank you very much!