The strand bias here means the genotypes inferred from info presented by the forward strand and the reverse strand disagrees. For example,
read depths data at a position after mapping could be
forward reverse
ref 20 33
alt 19 0
which shows strong strand bias.
My question is that how come this happen? I think there might be 4 possible causes:
Am I right? Any comments is welcome!
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wangyi2412
Have you seen this paper: http://www.biomedcentral.com/1471-2164/13/666? They argue that this is likely to happen at option #4, mainly because of interference between local realignment and BAQ steps. The primary cause of this could be a sequencing error.
This question was also discussed in the community (http://seqanswers.com/forums/showthread.php?t=9354), which argues that a specific CCGG motif causes bases to be skipped on one strand, but not the other. As far as I remember, Illumina is likely to produce Indels in Poly-G regions, and Indels are common case for incorrect variant calling.
PS It would be also very useful if you'll specify what sequencing system, read alignment software and variant caller you're using
Thank you! Sorry I reply late cause I did not have the Internet access.
Yes, the CCGG motif is a good hint! I will read it. Thank you very much!
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wangyi2412
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Possibility 1 is pretty low probability. You forgot #5, PCR duplication that didn't get marked.