Mutation discovery

[wrapapu]

I have a partial reference and multiple .fastq files containing different short reads of the same sample (the sample corresponds, of course, to the entire genome, while the reference is partial).

What tool should I use to determine mutations that are new in comparison to the reference? Is MAQ a good choice?

Is there a way to filter the read files so as to be able and store only the reads that map to my reference?

Thanks!

[bair]

Bwa for alignment, samtools for the rest work.