####Downloading and compiling

git clone git://github.com/lh3/alktk.git
(cd alktk; gcc -g -O2 -Wall -lz -o alktk alktk.c)

####Generating .alk files

ALK files are generated with a special version of samtools, which has not been pushed to the official github as a lot of development is happening there. The command line is:

bcftools view -cuI -K out.alk in.bcf > /dev/null 2>&1

Here the reference allele in out.alk is the allele used for generating the .bcf file.

####Viewing .alk files

alktk cat -t in.alk      # output entire file
alktk cat -tp in.alk     # only print positions and the reference allele frequency

In the full output, each line consists of 1) chromosome index, 2) position, 3) ML estimate of the reference allele frequency and 4) L(k) = Pr{d | there are k reference alleles}, for k=0,...,M, where M is the number of chromosomes in the samples.

####Subsetting .alk files

alktk sites in.alk in.srt.list > out.alk

where in.srt.list is a TAB delimited file with each line consists of 1) index of the chromosome, 2) position and 3) whether the reference allele in the original .bcf is the ancestral allele. This file must be position sorted. An example of in.srt.list is:

1   123456  0
1   234567  1
2   12345   0

This command flips the reference allele if it is not ancestral. In the output, the reference allele is the ancestral allele.

####Estimating AFS with EM

alktk afs in.alk > iter-1.txt              # starting from a flat prior
alktk afs in.alk iter-1.txt > iter-2.txt
alktk afs in.alk iter-2.txt > iter-3.txt

Here in.alk is typically the .alk on a list of sites, generated by alktk sites. Each afs command does one round of EM. The output gives the reference allele frequency.