Mapping for all alignments and allowing fewer mismatches

Question

[prawat2009]

Hello All,

I am trying to map 37bp reads of exome sequencing data to human genome. I have tried bowtie2 but it gives maximal 48% alignment rate. I further have to use these alignments for SNP calling. I want to try to allow maximum mismatches to be reported and all alignments. Please guide for further variations I can do, I have tried --very sensitive local option, also have tried to manipulate -ma and -mx options but alignment rate is similar or less.

Also, which other aligner can I use for this purpose?

Thanks

Priyanka