Quick Start

Whats on this page

There is also an elaborate tutorial here Tutorial

This page will contain som random examples which can be used as a quickstart.

Examples

Assuming you have a list of bamfiles in in file: 'list.txt' and you want the genotype likelihoods for position 12500000 on chromosome 8.

./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results -doGlf 1

This is using the SAMtools model for calculating genotype likelihoods (see genotype likelihoods for other models). Without the '-doGlf' parameter the genotype likelihoods will solely be estimated but will not be dumped. Therefore we also supply the '-doGlf 1' which will dump the genotype likelihoods as binary see GL outputs.