finding SNPs using aligments!

[biouser]

Hi all,

im trying to find SNPs in alignments after aligning reads using alignments softwares such as bowtie. does samtool find SNPs? if not can you introduce some powerfull and free softwares that find SNPs using inputs with "sam" or "bam" format?

thanks in advance.

[adaptivegenome]

Please take a little time to search SEQanswers before posting these kids of general questions.

[ECO]

I am closing this. Please have the courtesy to search before asking the most basic questions.