SNP Calling for 454 reads

[empyrean]

I would like to call SNP's and indels from my data which has 30 samples of which 20 samples are of one genotype and other 10 are from other genotype. I have a reference sequence which is a 1 mb qtl sequence. Which is the best way to call SNP's? I tried Mosaik but its aligning approximately 50% of reads and also bwa-sw which aligns ~90-95% of my reads. so i thought of using samtools / mpileup and bcftools as told at this link and this link

But my concern is how to differentiate with my genotypes? changing read names accordingly and where can i specify to consider 20 as one group and 10 as another group to classify SNPs? Suggestions please..

[empyrean]

any suggestions?