Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Difference between and strict_strand strand bias in vcf files generated by FilterMutectCalls


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    David Benjamin

    Leo Hsiao The strict strand bias filter is only used for the Broad's duplex sequencing pipeline or similar applications with an extreme preference for precision at the expense of sensitivity.  It is inactive by default, though it shows up in the VCF header.  Just continue to run FilterMutectCalls with default settings and this extra filter won't cause any trouble.

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