Population Rate Calculation Programme

Question

[jackuser1979]

I have RNA seq of illumina paired reads mapped to reference genome (bam file) and VCF file from variant calling software. I would like to calculate population mutation rate (theta). Is there any good available programme or scripts already available?

Answer 1

[Zev.Kronenberg]

I would not suggest calculating the population mutation rate with RNA data. WGS would be your best bet. your estimate of theta will be much lower if you are just considering mRNA.