Thanks for the information. I also post this question to GATK community, and there is an extensive discussion on this topic. And here is the link:
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Check this thread : http://seqanswers.com/forums/showthread.php?t=9354Leave a comment:
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strand bias variant call
We found some heterzygous calls. When we checked in IGV, the reads with reference base are balanced between plus strand and minus strand, however, the reads with alternative base are only mapped to minus strand or plus strand. In which way the reads with alternative base can be so biased? The mapping quality are OK for these reads.
It could be alternative allele only be sequenced on one strand but for reference allele, both strand are sequenced. Is it possible like this if the experiment is not designed so?
Or, these alternative alleles are artifacts. But what could be the reasons to generate these artifacts?
Thanks for any feedback/discussion.
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