This workflow converts csfasta and qual files into a fastq file, runs bwa (using colorspace index), samtools mpileup and bcftools to identify SNPs. The SNPs are then compared to dbSNP to identify annotation.
Import this workflow here: http://prandtlseq.icmb.utexas.edu/u/dhivyaa/w/bwasamtools
(If you're looking for the command-line equivalent, check out the ?SAMTOOLS page)