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Hi. Could you suggest a recommended pipeline for us. We receive BAM files from our sequencing - the sequencing is mostly targetted regions (~10MB) and the species is dog, so we don't want to skip known SNPs as different breeds have different known SNPs. We have one BAM file for each dog sample, usually about 10 samples.
I have looked at the guidelines (Best Practice Variant Detection) for this but I'm a bit confused...