Quick Start

This page contains some random examples that shows some aspect of the ANGSD program. There is also an old Tutorial, but this is somewhat outdated.

Whats on this page

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.