Can anyone suggest an optimum data processing pipeline for analysing dog next gen sequencing data. We start with BAM files, and generally have about 5 cases and 5 controls. (10 samples = 10 BAM files). We don't want to ignore known SNPs since different breeds have different SNPs.
Is there a way to analyse all the BAM files in parallel so that information from all of them can be used in producing aligned cleaned deduped BAM files?
Is there a way to analyse all the BAM files in parallel so that information from all of them can be used in producing aligned cleaned deduped BAM files?
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