SNP calling from a reference sequence

[blackrabite]

Hello, I am looking for SNPs in the rDNA of fungal genomes.
I have a consensus sequence (~100 bps), and a lot of reads taken from a WGS (~900 bps) that align to it, the reads are provided together with their quality scores.
I'd like to look for SNPs among these reads, is there a software ready to use or should I write one by myself? I have seen MAQ, but it seems it works only with short reads. Do you have any suggestions?

thank you

[blackrabite]

I forgot to say that I am mostly interested in variations than indels

Hello, I am looking for SNPs in the rDNA of fungal genomes.
I have a consensus sequence (~100 bps), and a lot of reads taken from a WGS (~900 bps) that align to it, the reads are provided together with their quality scores.
I'd like to look for SNPs among these reads, is there a software ready to use or should I write one by myself? I have seen MAQ, but it seems it works only with short reads. Do you have any suggestions?

thank you

[monad]

GSNAP/GMAP works very well for us. Here is the link.

http://research-pub.gene.com/gmap/