Calculating Watterson's Theta and Tajima's Pi from NGS (bam file)

Question

[Adrian Pelin]

Hello,

I am currently using PoPoolation to calculate Tajima's Pi and Watterson's Theta from my reference aligned reads (bam file). However, even at 100x coverage the script is slow, can take several days to parse one 160kb contig.

Any ideas on faster tools? I am working with non model organisms.

Adrian

[Istvan Albert]

Off topic: I will add PoPoolation to Crac: Funny And/Or Weird Names For Bioinformatics Tools