Count of read pairs in the F1R2 and F2R1 configurations supporting REF and ALT alleles (F1R2, F2R1)
Category Variant Annotations
OverviewCount 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.
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
GATK version 220.127.116.11 built at 25-51-2019 10:51:39.