ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
Quick Start: Difference between revisions
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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 There is also an old [[Tutorial]], but this is somewhat outdated.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== | ==Whats on this page== | ||
This page will contain som random examples which can be used as a quickstart. | This page will contain som random examples which can be used as a quickstart. | ||
Revision as of 23:18, 17 December 2013
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 There is also an old Tutorial, but this is somewhat outdated.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.