Showing docs for version 3.6-0 | The latest version is 4.1.4.0


OxoGReadCounts

Count of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate alleles

Category Annotation Modules

VCF Field FORMAT (sample genotype-level)


Overview

This is an annotation that gathers information about the read pair configuration for the reads supporting each allele. It can be used along with downstream filtering steps to identify and filter out erroneous variants that occur with higher frequency in one read pair orientation.

References

For more details about the mechanism of oxoG artifact generation, see "Discovery and characterization of artefactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation." by Costello et al.

Caveats

  • At present, this annotation can only be called from MuTect2
  • The FOXOG annotation is only calculated for SNPs

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.