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Old 09-21-2016, 10:08 PM   #1
antifolate
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Location: Chesterfield, MO

Join Date: Aug 2015
Posts: 52
Default Need help understanding what "b-allele" refers to

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:
Code:
   
--b-allele-vcf=VALUE   vcf containing SNV b-allele sites (only sites 
                               with PASS in the filter column will be used) 
                               (required)
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?
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