Thread: SNP calling
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Old 12-19-2012, 11:46 AM   #1
Location: California

Join Date: Feb 2011
Posts: 32
Default SNP calling

Reference-based SNP callers work by comparing the sequence aligned to the reference. Are there any tools/piplines that will call SNPs between aligned files? In my case I am interested in calling SNPs between the genotypes I am aligning and not in SNPs present between by genotypes and the reference.
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