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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./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results | ./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results | ||
</pre> | </pre> | ||
This is using the SAMtools model for calculating genotype likelihoods see [[Genotype likelihoods]] for other models. | This is using the SAMtools model for calculating genotype likelihoods see [[Genotype likelihoods from alignments | genotype likelihoods]] for other models. | ||
Revision as of 09:08, 23 October 2012
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
This is using the SAMtools model for calculating genotype likelihoods see genotype likelihoods for other models.