I'm trying to call nucleotide diversity for a pool-seq dataset using PoPoolation's
Variance-sliding.pl. However it's taken over a day to run one chromosome. I want to speed this up,
Does anyone know how to multi-thred PoPoolation, or other tips that could get it running quicker?
perl popoolation_1.2.2/Variance-sliding.pl --input in.mpileup --output out.varslid.pi \ --measure pi --min-count 2 --min-qual 20 --min-coverage 50 --pool-size 100 \ --window-size 1000 --step-size 1000