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I'm trying to work with Canvas to find Copy Number Variants in human data. I would appreciate if someone clarified what this input is supposed to be:
I have called and filtered SNPs for my samples. Is this asking me to provide the set of SNPs (or SNP sites) that are flagged as having the alternate allele in the VCF file? If so, couldn't I just grep AB=1 and be good?
Code:
--b-allele-vcf=VALUE vcf containing SNV b-allele sites (only sites
with PASS in the filter column will be used)
(required)