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?
<p>Just use one of the presets, likely either <code>--very-sensitive</code> or <code>--very-sensitive-local</code>. If you&#39;ve not trimmed the reads (or just trimmed off adapters), then you should use local alignment. If, however, you&#39;ve adapter &amp; quality trimmed the reads, then using end-to-end alignment would seem more relevant. Realistically speaking, you should get very similar results (from variant calling) regardless. In general, local alignment will sometimes give a bit better results, since you can still get alignments in cases of structural rearrangements or variants at the end/start of reads.</p>
