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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==Genotype calling== | ==Genotype calling== | ||
The program can do genotype calling in different tempis. | |||
output file .geno | output file .geno | ||
-doGeno 1, print out major minor | ;-doGeno 1:, print out major minor | ||
-doGeno 2, print the called genotype under HWE (suyeon maf prior method) | ;-doGeno 2:, print the called genotype under HWE (suyeon maf prior method) | ||
-doGeno 4, print out the genotype with the best raw likelihood | ;-doGeno 4:, print out the genotype with the best raw likelihood | ||
-doGeno 8, print out the posteriour under the suyeon model | ;-doGeno 8:, print out the posteriour under the suyeon model | ||
-doGeno 16, print all 3 posts (major,major),(major,minor),(minor,minor) | ;-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 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 | ;-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 | 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 12:18, 19 June 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 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