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.
Genotype calling
Genotype calling
The program can do genotype calling in different tempis.
output file .geno
- -doGeno 1
- , print out major minor
- -doGeno 2
- , print the called genotype under HWE (suyeon maf prior method)
- -doGeno 4
- , print out the genotype with the best raw likelihood
- -doGeno 8
- , print out the posteriour under the suyeon model
- -doGeno 16
- , print all 3 posts (major,major),(major,minor),(minor,minor)
- -doGeno 32
- , print the depth, (if availble), the number of reads used to determine the genotype llhs.
- -doGeno 64
- , somewhat different dumps the binary posts for all samples, encoded as 3*nind double
The genotype are integers such that AA=0,AC=1,AG=2,AT=3,CC=4,CG=5,CT=6,GG=7,GT=8,TT=9
output is (-doGeno NOT 64) chr, pos, numberof samples times[ the above]
NB currently you also need to supply -doMaf to run this genotype calling