Question: What's the possible causes of strand bias in exome sequencing?
gravatar for wangyi2412
5.6 years ago by
wangyi2412220 wrote:

The strand bias here means the genotyped infered from info presented by the forward strand and the reverse strand disagress. 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:

1 the sample itself does not strickly base paired

2 exome capture bias ( how could this happen? )

3 sequencing error(how could this happen?)

4 mapping error

Am I right? Any comments is welcome! 

strand bias ngs exome • 8.0k views
ADD COMMENTlink modified 5.6 years ago by mikhail.shugay3.4k • written 5.6 years ago by wangyi2412220

Possibility 1 is pretty low probability. You forgot #5, PCR duplication that didn't get marked.

ADD REPLYlink written 5.6 years ago by Devon Ryan94k
gravatar for mikhail.shugay
5.6 years ago by
Czech Republic, Brno, CEITEC
mikhail.shugay3.4k wrote:

Have you seen this paper: 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 (, 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

ADD COMMENTlink written 5.6 years ago by mikhail.shugay3.4k

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!

ADD REPLYlink written 5.5 years ago by wangyi2412220
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