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 | ./angsd -outfiles out -doMaf 16 -beagle file.beagle | ||
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Revision as of 18:02, 14 June 2012
ANSGD currently supports various mapped data, genotype likelihood formats and imputed genotype probability files
Mapped sequence file
bam files
soap files
genotype likelihood files
glfv3
genotype probability files
beagle format
Genotype probabilities in beagle format can be used as input. The format used is the haplotype imputation format outputted from beagle [1].
options
To include a beagle file us the option
- -beagle [file]
example
The file format is a single linje per site. The first 3 coloums are
- markerName
- alleleA
- alleleB
For each individual 3 coloums are added. These three colums should sum to one.
Example of a file with two individuals
marker alleleA alleleB NA06984 NA06984 NA06984 NA06986 NA06986 NA06986 chr9_95759065 G A 0.6563 0.3078 0.0358 0.5357 0.4016 0.0627 chr9_95759152 C A 1 0 0 0 1 0 chr9_95762332 G A 0.925 0.0734 0.0015 0.894 0.1031 0.0029 chr9_95762333 A T 0.8903 0.1067 0.003 0.811 0.1797 0.0093 chr9_95762343 G T 0.9149 0.0835 0.0017 0.8396 0.1541 0.0064
Example of estimating allele frequencies from beagle files
./angsd -outfiles out -doMaf 16 -beagle file.beagle