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