Question: What Is The Vcf-Compliant Way Of Specifying Copy Number Values For Tumor/Normal Analysis?
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gravatar for 14134125465346445
6.0 years ago by
United Kingdom
141341254653464453.5k wrote:

What is the VCF-compliant way of specifying that a region of a chromosome contains a given copy number value in the tumor and a given copy number value in the normal?

Reading the specification (http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41) I understand that the copy numbers have to be specified with the CN tag:

##INFO=<ID=CN,Number=1,Type=Integer,Description="Copy number of segment containing breakend">

But how should the tumor/normal info be written? Can I have an example vcf file where chromosomal segments in the tumor have a different CN to the normal? And is there any toolkit that will validate CN information in a VCF to say if it abides by the spec?

vcf software cnv • 1.6k views
ADD COMMENTlink modified 6.0 years ago by Sean Davis25k • written 6.0 years ago by 141341254653464453.5k
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gravatar for Sean Davis
6.0 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

I think the FORMAT CN tag, which allows you to assign a copy number to each sample individually, might satisfy your needs.

ADD COMMENTlink written 6.0 years ago by Sean Davis25k
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