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 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