SamTools and allelic expression

[ameyer]

Hi,
I have RNA-seq reads from Illumina and I have used TopHat to align them. I have reads from two inbred parents and two hybrid offspring. I have used SamTools mpileup to find SNPs between the two parents and want to use these SNPs to find allelic expression differences in the hybrids. Is there an easy way to do this? Can an input file containing the SNPs be given to SamTools?
Thanks

[volks]

you could align the offspring data using TopHat and then use:
samtools mpileup -l FILE ..list of positions (format: chr pos) [null]
at the positions where you found SNPs in the parents. the ratio will tell you the expression differences.

there might be better solutions ..