how to identify if RNAseq data is from same patient

Question

[datanerd]

HI all,

I have RNAseq data from the same pateint before and after treatment. If I had to check if they are the same individual- how do i do this based on RNAseq data. Call variants and see? Please suggest of any ways of doing it.

Thanks, mamta

Answer 1

[Shicheng Guo]

Don't call the SNP genome-widely, since there will be large number sudo-SNPs caused by RNA-edit. What you need to do it check the status of the 100,000 classic high frequent SNPs (Download it from UCSC) and then you can do the cluster analysis. I think it is power enough to identify the same individual.

[datanerd]

Thanks Shicheng. I will try doing that. Any specific program that you could suggest to call variants?

[andrew.j.skelton73]

Depending on your depth, GATK is probably your best bet

Answer 2

[John]

You probably thought of this already, but if one sample has a Y chromosome and one does not, thats a pretty big give-away.