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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

Mutect2 : annotation group & fields that can check strand bias


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    David Benjamin

    FOXOG was an orientation bias annotation, which is not quite the same thing as strand bias.  In any case Mutect2 hasn't emitted this annotation for quite a while.  Mutect2's default strand read count annotation is StrandBiasBySample (SB).  FilterMutectCalls contains a strand artifact model that internally calculates the probability that an allele is a strand bias artifact.  In addition to possibly applying a strand bias filter, it applies a STRANDQ annotation denoting the phred-scaled probability that a variant is a strand artifact.

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