I think many people are confused about strand bias and orientation bias, especially when after reading the mutect.pdf in github docs. here is some description in it
The strand artifact filter detects sequencing artifacts in which the evidence for the alt allele consists entirely of forward strand reads alone or reverse strand reads alone.
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.
ngs will sequence top and bottom strand , both strand has its own read1 and read2. ofcourse, either reads1 or reads2 will be mapped to top or bottome each, so it must can also be called F1R2 or F2R1 for the paired reads1 and reads2.
as you said in mutect.pdf, it is obvious strand bias and orientation is almost the same.
or can you point out reads1 and reads2 . F1R2 F2R1 reads, orientation bias and strand bias in one screenshot
thanks a lot
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