ANGSD: Analysis of next generation Sequencing Data
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Introduction: Difference between revisions
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===Whats on this page=== | |||
This page will contain som random examples. | |||
==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. | Assuming you have a list of bamfiles in in file: 'list.txt' and you want the genotype likelihoods for position 12500000 on chromosome 8. | ||
<pre> | <pre> | ||
./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results | ./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. | This is using the SAMtools model for calculating genotype likelihoods (see [[Genotype likelihoods from alignments | 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 [[Genotype_likelihoods_from_alignments#output_genotype_likelihoods |GL outputs]]. | ||
Latest revision as of 18:13, 23 October 2012
Whats on this page
This page will contain som random examples.
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.