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Test-drive the GATK tools and Best Practices pipelines on Terra

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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 ?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The best way to filter out variants that are poorly supported is doing VQSR (variant recalibration) as detailed in our Best Practices. Another way is to increase the calling confidence thresholds.

    If you really want to exclude low quality bases upfront, you can use the --min_base_quality_score / -mbq ( int with default value 17 ) argument. See the Technical Documentation for details.

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