I am fairly new to exome sequencing and not familiar with tools available for analysis of this kind of data. I need to calculate from an exome sequencing dataset that I aligned using BWA, the equivalent of FPKM/RPKM for RNAseq data. I was wondering if there was any kind of tool that I could use directly (e.g cufflinks for RNA-seq) that would give me this info.
Any help is appreciated.
Please be specific.. what are you trying to find? call variants?
Hi I am not looking to call variants. I already know how to do that..but am just looking for coverage(?) of specific genes...just like you get FPKM for genes in RNA-seq.
Thank you all. I will try out your suggestions. They were very helpful.
You are welcome. For next time, probably better to add your thank you as a comment on one of the answers or as a comment to your original question, rather than as an "answer" to your question.