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.
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(Created page with "==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.tx...") |
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<pre> | <pre> | ||
./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results -doGlf 1 | ./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results -doGlf 1 | ||
<pre> | </pre> | ||
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. | 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. | ||
Revision as of 20:14, 23 October 2012
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.