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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Is it possible not to take low quality into account while calling snps ?
I have used
UnifiedGenotyper to call SNPS. I found some SNPs that has been reported from low quality reads in chromosome X and chromosome Y. Is it possible not to take low quality reads into account while calling SNPs using
UnifiedGenotyper? Or, do I need to do quality filtering of BAM files before hand ?