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Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data
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Canvas:REF #133

Closed oalavijeh closed 5 years ago

oalavijeh commented 5 years ago

Dear Canvas team,

I have multiple "structural" VCFs made up of Manta and Canvas calls merged into a per patient VCF. Looking at the files the IDs are made up of MantaDEL, Canvas:GAIN etc which make sense. However, there are a few Canvas:REF calls made and I was unsure what these meant? I wasn't too clear from the notation at the end of your readme.

Many thanks for your help

Omid

eroller commented 5 years ago

Canvas:REF would mean, not variant, i.e. copy neutral. I believe Manta does not emit REF calls, just variant calls?

oalavijeh commented 5 years ago

Thanks! Yes Manta does not have REF calls.

All the best