Consensus/SNP/indel calling with samtools
After creating a SAM-format alignment of next-gen, or even Sanger sequences to a reference (via maq, bwa, bowtie, SOAP, etc.), we commonly want to call a new consensus, or identify homo- or heterozygous SNP positions or indels. This can be done using samtools. Samtools incorporates the maq model for new consensus calling.
A brief set of commands for doing this ... i.e. variant detection and filtering, can be found here, within the samtools pages.
A more in depth walkthrough, that incorporates some more stringent filtering, can be found in this FAQ put together by Heng Li, who is the author of maq and bwa, and a contributor to the SAM format specification.