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

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OxoGReadCounts Follow

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GATK Team
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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

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GATK version 4.0.3.0 built at 02-29-2019 02:29:33.

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