I'm using Bowtie2 for mapping reads to human genome. I'm using Bowtie2 first time, so what are the best parameters to set if we are using these mapping results to further use to detect SNPs? bowtie2 has also given some preset options. which is more appropriate for finding SNPs from alignment results.

Which one is more appropriate local or end-to-end mode? if my purpose of alignment is SNP detection?
After what Devon say about trimming

What I am using

    $BT2_HOME/bowtie2 --local -x specious -U $BT2_HOME/example/reads/longreads.fq -S eg.sam

`-U` Comma-separated list of files containing unpaired reads to be aligned, e.g. `lane1.fq,lane2.fq,lane3.fq,lane4.fq`. Reads may be a mix of different lengths. If `-` is specified, `bowtie2` gets the reads from the "standard in" or "stdin" filehandle.

`-x` The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final `.1.bt2` / `.rev.1.bt2` / etc. `bowtie2` looks for the specified index first in the current directory, then in the directory specified in the `BOWTIE2_INDEXES` environment variable.

`-S` File to write SAM alignments to. By default, alignments are written to the "standard out" or "stdout" filehandle (i.e. the console).

If your data not indexed use

    $BT2_HOME/bowtie2-build -f ~/path/to/your/genome.fa ~/where/you want/index/to/be/nameOfTheIndex

summary of the parameters: http://chipster.csc.fi/manual/bowtie2-paired-end.html

for more visit http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml