I'm analysing exome dataset, I performed the alignment and variant calling with different tools BWA-MEM, Bowtie2, Cushaw3, Novoalign. Variant calling by Freebayes and GATK-HC. How can I conclude which aligner is the best, on what parameters ? I feel, 1) Alignment percentage (no. of PE reads mapped against reference) 2) Computation time
Can you give me a strong answer.