Question: Calculating Watterson's Theta and Tajima's Pi from NGS (bam file)
2
gravatar for Adrian Pelin
4.2 years ago by
Adrian Pelin2.2k
Canada
Adrian Pelin2.2k wrote:

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

snp theta pi bam ngs • 3.1k views
ADD COMMENTlink written 4.2 years ago by Adrian Pelin2.2k
1

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

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 80k
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