Population-analysis-with-pooled-data

This repository contains python scripts for analyzing population data from pooled sequencing.

AF_per_pool.py

Calculate allele frequency for each sample given AD format out of vcftools.
Allele frequency is based read count.
python AF_per_pool.py file.AD.FORMAT > file.freq

chi_square_contrast.py

Chi-square test of allele depth at each SNP.
chi_square_contrast.py --popA POPA --popB POPB --AD AD
The following arguments are required: --popA, --popB, --AD
popA and popB are the lists of contrasting samples. One sample per row.
AD is the allele depth after correction of population size.

DAF_Categorical_SNP.py

Count the number of SNPs in each genomic category of each binned delta allel frequency.
DAF_Categorical_SNP.py --DAF DAF --Anno ANNO [--Bin BIN]
The following arguments are required: --DAF, --Anno
DAF is the file of delta allele frequency at each SNP.
Anno is the annotate SNP file out of snpEff. The default bin value is 0.1

deltaAF.py

Calculate delta allele frequency between the given populations.
deltaAF.py --popA POPA --popB POPB --freq FREQ
popA and popB are the lists of contrasting samples. One sample per row.
freq is the corrected allele frequency file (For example, 60.Neff.freq)

Neff_correction.py

Correct allele depth based on sample size.
Neff_correction.py sample.list pool.AD.FORMAT > pool.Neff.freq
Example of sample list:
ID Size
A 47
B 50
C 49
D 35
...

MAF.py

Calculate minor allele frequency for certain samples of pooled data.
MAF.py --pop POP --AD AD
The following arguments are required: --pop, --AD
--pop flag can be specified multiple times