You might use different mappers
We will consider BWA and Bowtie2 More information about BWA: http://bio-bwa.sourceforge.net/bwa.shtml More information about bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
BWA is slower but more accurate than BWA. BWA mem is more SNP tolerant and also showed the best tolerance to indels.