<p>What are chimeric reads? Is there any effective method to distinguish chimeric reads from normal ones? Can someone point me to a survey or reviews on that topic? Thank you a lot!</p>

<p>Zhen</p>

Chimeric reads occur when one sequencing read aligns to two distinct portions of the genome with little or no overlap. Chimeric reads are indicative of structural variation. Chimeric reads are also called split reads.

After aligning with bwa mem, chimeric reads will have an SA tag as described on page 7 of the [SAM format specification][1]. To find them all you have to do is extract them using grep.

    samtools view my_alignment.bam | grep 'SA:' | less

For reference:

 - [Identification of genomic indels and structural variations using split reads][2]
 - [Genome structural variation discovery and genotyping][3]


 [1]: http://samtools.github.io/hts-specs/SAMv1.pdf
 [2]: http://www.biomedcentral.com/1471-2164/12/375/
 [3]: http://www.nature.com/nrg/journal/v12/n5/abs/nrg2958.html