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: Difference between revisions
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;-doGeno 1:, print out major minor | ;-doGeno 1:, print out major minor | ||
;-doGeno 2:, print the called genotype | ;-doGeno 2:, print the called genotype as 0,1,2 | ||
;-doGeno 4:, print | ;-doGeno 4:, print the called genotype as AA, AC, AG, ... | ||
;-doGeno 8:, print | ;-doGeno 8:, print all 3 posts (major,major),(major,minor),(minor,minor) | ||
;-doGeno 16:, print | ;-doGeno 16:, print the posterior of the called genotype | ||
;-doGeno 32 | ;-doGeno 32:, 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 | 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 |
Revision as of 18:38, 10 October 2012
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 as 0,1,2
- -doGeno 4
- , print the called genotype as AA, AC, AG, ...
- -doGeno 8
- , print all 3 posts (major,major),(major,minor),(minor,minor)
- -doGeno 16
- , print the posterior of the called genotype
- -doGeno 32
- , 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