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 output.

There are 3 approaches for making plink file. First is based on calling genotypes with angsd and outputting the results as a .tped file. The second approach is a based on doing a pseudohaploid call for sites for a list of individuals followed by a subprogram for converting this into a .tped file. Final approach is based on generating a fasta file (which also contains the pseudo haploid concensus) for each individual followed by a subprogram that extract the reference bases for specific sites and is then merged into a tped file.

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

Brief Overview

------------------------
writePlink.cpp:
	-doPlink	0
	1: binary fam/bim/bed format (still beta, not really working)
	2: tfam/tped format

	NB This is a wrapper around -doGeno see more information for that option

Example

A full example commandline is given below:

 ./angsd -bam bam.filelist -out outnames -doPlink 2 -doGeno -4 -doPost 1 -doMajorMinor 1 -GL 1 -doCounts 1 -doMaf 2 -postCutoff 0.99  -SNP_pval 1e-6 -geno_minDepth 4

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

Output files

The above commands will generate a .tfam/.tped files

output.tfam

1 1 0 0 0 -9
2 1 0 0 0 -9
3 1 0 0 0 -9
4 1 0 0 0 -9
5 1 0 0 0 -9
6 1 0 0 0 -9
7 1 0 0 0 -9
8 1 0 0 0 -9
9 1 0 0 0 -9
10 1 0 0 0 -9
11 1 0 0 0 -9
12 1 0 0 0 -9
13 1 0 0 0 -9
14 1 0 0 0 -9
15 1 0 0 0 -9
[capped]

output.tped

1 1_14000202 0 14000202 G G     G G     G G     G A     G G     G G     G A     G A     G A     G G     G G     G A     G G     G G     G A     G A     G G     G G     G G     G A     G G     G G     G A     G G     G G     G G     G G     G G     G A     G G     G A     G A     G G
1 1_14000873 0 14000873 G G     G G     G G     A A     G A     G G     G G     G G     G A     G G     G A     G G     G A     G G     G G     A A     G G     G A     G G     G A     G A     G G     G A     G G     G G     A A     A A     G G     G A     G G     G A     G G     G G
1 1_14001018 0 14001018 T T     T T     T T     C C     T C     T T     T T     T T     T C     T T     T C     T T     T T     T T     T T     C C     T T     T C     T T     T T     T C     T T     T T     T C     T T     T C     T C     T T     T C     T T     T C     T T     T T
1 1_14001867 0 14001867 A A     A A     A A     A G     A G     A A     A A     A A     A G     A A     A G     A A     A G     A A     A A     G G     A A     A G     A A     A G     A G     A A     A G     A G     A A     A G     G G     A A     A G     A A     A G     A A     A A

Notice that the family id simply an incrementing integer, and that the SNPid is the genomic position.

NB

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

References

[1]