Showing tool doc from version 4.1.2.0 | The latest version is 4.1.2.0

OrientationBiasReadCounts

Count of read pairs in the F1R2 and F2R1 configurations supporting REF and ALT alleles (F1R2, F2R1)

Category Variant Annotations


Overview

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

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, doi: 10.1093/nar/gks1443


Return to top


See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum

GATK version 4.1.2.0 built at Tue, 23 Apr 2019 14:55:55 -0400.