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. To find them all you have to do is extract them using grep.
samtools view my_alignment.bam | grep 'SA:' | less
Chimerism condition in which a gene is formed from combination of two other genes. Suppose part of your gene is matching to one gene ( also of species) and other part is matching to other gene (also can be from different species).
If you want to detect chimerism in your sequence, the simplest way is to match your gene to NCBI or any other database. Then check the alignment hits. If there chimerism exists, part of your gene will match to different genes.
A simple explanation:
Chimeric reads is the sequence form through the combination of portions of one or more coding sequences to produce new genes.