I was wondering what is the difference between BWA mem, sampe and bwasw options for aligning paired-end data. I have PE data with the read length ~100 bp before trimming for whole exome analysis. I am aligning them using the following command:
bwa mem -t 4 -M L001_R1_001_trimmed.fq L001_R2_001_trimmed.fq > L001.sam
I am wondering if
- The above command is OK for paired-end data?
- BWA mem is the best option for this?