Monday, 27 September 2021

Orientation Bias artifect

 strand bias and orientation bias – GATK (


The read orientation artifact, also known as the orientation bias artifact, arises due to a chemical change in the nucleotide during library prep that results in, for example, G base-paring with A. This kind of artifact has a clear signature (e.g. C to A SNP that occurs predominantly for the middle C in the DNA sequence CCG), and it’s singlestranded in nature. Downstream, this artifact manifests as low allele fraction SNPs whose evidence for the alt allele consists almost entirely F1R2 reads or F2R1 reads. A read pair is F1R2 (forward 1st, reverse 2nd) if the sequence of bases in Read 1 maps to the forward strand of the reference (F1), and the sequence of Read 2 to the reverse strand
of the reference (R2). F2R1 is defined similarly


if someone has read the dragonbioit used guide in illumina, it just mentioned orientation bias, ignore the strand bias.


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