SNP calling from transcriptome data

[lre1234]

Hi all,

I am interested in trying to make SNP calls from RNA-seq data. Has anyone had experience doing this? I assume that it would be similar to DNA-seq and a program such as samtools would work. Is there any other application that might also be useful to try?

thanks for your help

[mathew]

SNPs

I believe you are right you should be able to use sam tools pileuo option after aligning reads

[steven]

Doesn't the GATK work too?