popoolation2helper

calculate allele frequency and allele frequency difference using sync data format generated by popoolation2

popoolation2 https://sourceforge.net/p/popoolation2/wiki/Tutorial/ is a very useful tool for Pool_seq data, and can generate sync format file which contains the allele count for each population and each polymorphic site. But unfortuately, it can't output allele frequency for specific population. Although it can produce allele frequency difference, it calculates across all pairwise populations, and generate very large files with some data your don't want to use.

This tool exploits the sync data, but it allows you to specify the populations you want to calculate allele frequency, and allows you to specify the population pairs you want to compare allele frequency difference without necessary to output difference across all populations.

Input data format

sync data (refer to popoolation2 tutorial) format as following:

2L	1524	T	0:200:0:2:0:0	0:202:0:0:0:0	0:202:0:0:0:0	0:202:0:0:0:0	0:202:0:0:0:0
2L	1669	G	2:0:0:200:0:0	3:0:0:199:0:0	31:0:0:171:0:0	23:0:0:179:0:0	15:0:0:187:0:0
2L	1675	A	200:0:0:2:0:0	202:0:0:0:0:0	202:0:0:0:0:0	202:0:0:0:0:0	202:0:0:0:0:0
2L	2821	C	0:2:200:0:0:0	0:0:202:0:0:0	0:0:202:0:0:0	0:0:202:0:0:0	0:0:202:0:0:0
2L	2965	T	0:200:0:2:0:0	0:202:0:0:0:0	0:202:0:0:0:0	0:202:0:0:0:0	0:202:0:0:0:0
2L	2980	G	2:0:0:200:0:0	0:0:0:202:0:0	0:0:0:202:0:0	0:0:0:202:0:0	0:0:0:202:0:0
2L	3066	T	0:200:0:2:0:0	0:197:0:5:0:0	0:202:0:0:0:0	0:202:0:0:0:0	0:202:0:0:0:0
2L	3067	T	0:200:2:0:0:0	0:197:5:0:0:0	0:202:0:0:0:0	0:202:0:0:0:0	0:202:0:0:0:0
2L	3068	C	2:0:200:0:0:0	5:0:197:0:0:0	0:0:202:0:0:0	0:0:202:0:0:0	0:0:202:0:0:0
2L	3069	A	200:2:0:0:0:0	197:5:0:0:0:0	202:0:0:0:0:0	202:0:0:0:0:0	202:0:0:0:0:0

Making sure you have valid reference allele in column 3.

Install

Download the source files, and then compile the source code directly; or using:

chmod 777 install.sh
./install.sh

It will generate two executable object: calfreq and caldiff.

Usage

1. calculate allele frequency

./calfreq -i test.sync -f 1,3,2,5 -d 0,999 -b 0 -m 0.05

-i specify input sync file;

-f specify the poplation you want to calculate allele frequency, 0 indicate all populations;

-d specify read depth, a biallelic site with a read depth between 0-999 for all populations(not only specified using -f) can be retained in the output file. default 0,999

-b specify if only keep biallelic sites. 1 indicates only keep biallelic sites, 0 indicates NOT check biallelic. default 0.

-m specify minor allele freqeucny(MAF) across all pops together. Alelel with second largest counts is regarded as minor allele. default 0.05.

2. calculate allele frequency difference

./caldiff -i test.sync -p 1-2,4-3,2-5 -d 0,999 -b 0 -m 0.05

-i specify input sync file;

-p specify the population pairs you want to compare allele frequency difference, each pair separated by ,;

-d specify read depth. default 0,999

-b specify if only keep biallelic sites. 1 indicates only keep biallelic sites, 0 indicates NOT check biallelic. default 0.

-m specify minor allele freqeucny(MAF) across all pops together. Alelel with second largest counts is regarded as minor allele. default 0.05.

3. calculate coverage for each site in each population

./calcov test.sync

This function will calculate the allele count of A/T/C/G in each site for each population. The outcome will be in test.sync.cov file.