Plink

From version 0.549 we now support plink output files. Currently we only support the transposed .tfam/.tped files. But we are working on a native .bed/.bim/.fam dumper.

This method is essentially a wrapper around the existing genotype caller, and all options for the genotype caller can therefore be used for the plink formated output file.

See Genotype calling for options relating to calling genotypes. For dumping the plink file you should supply:

-doPlink 2

A full example commandline is given below:

 ./angsd -bam smallBam.filelist -out outnames -doPlink 1 -doGeno -4 -doPost 1 -doMajorMinor 1 -GL 1 -nThreads 20 -doMaf 2 -postCutoff 0.9999  -minLRT 24 -doSNP 1

Notice the extra minus in the -dogeno -4 argument, this will suppress the -doGeno output.

NB

We highly recommand that users, don't perform analysis on called genotypes, since calling genotypes is likely to cause bias in the downstream analysis.