Genotype calling

The program can do genotype calling based either on the genotype til the highest likelihood or by using the frequency as a prior(recommended see Kim2011).

options

-doGeno [int]

1: print out major minor

2: print the called genotype as --1,0,1,2

4: print the called genotype as AA, AC, AG, ...

8: print all 3 posts (major,major),(major,minor),(minor,minor)

16: print the posterior of the called genotype

32: somewhat different dumps the binary posterior for all samples, encoded as 3*nind double

Use the sum of the above to give the output you want. Forexample -doGeno 5 (1+4) prins the major and minor allele followed by the genotype (AA, AC ...) for each individual

-doPost [int]

1: estimate the posterior genotype probability based on the allele frequency as a prior

2: estimate the posterior genotype probability assuming a uniform prior

-postCutoff [float]

Call only a genotype with a posterior above this threshold.

NB if the raw posterior dump is requested the -postCutoff is not used

example

./angsd -bam bam.filelist -GL 1 -out outfile -doMaf 2 -doSNP 1 -doMajorMinor 1 -minLRT 24 -doGeno 5 -doPost 1 -postCutoff 0.95

gives a output like this:

1       14000202        G       A       GG      NN      NN      GA      NN      
1       14000873        G       A       GG      GG      GG      AA      GA      
1       14001018        T       C       NN      NN      NN      CC      NN      
1       14001867        A       G       NN      AA      AA      NN      NN      
1       14002342        C       T       CC      CC      CC      CC      CC      
1       14002422        A       T       AA      NN      NN      NN      NN      
1       14002474        T       C       TC      TT      TT      TT      TT      
1       14003581        C       T       CC      CC      NN      NN      CT      
1       14004623        T       C       TT      TT      TT      NN      TC      
1       14005069        A       G       AA      AA      AA      AA      AA