This repository contains the code necessary to run the genome-wide allele frequency estimation from the data produced by grene-net.org consortium.
| SOFTWARE | TASK |
|---|---|
| skewer | Trimming & quality filter |
| fastqc | Visualize quality measurements |
| Bwa mem | Mapping to reference |
| Samtools | Alignment |
| IGV | Visualize alignment |
| bamfreq | Extract base counts per position |
| pool | Read two or more base count files and generate a fvcf |
All steps up until pool are wrapped in the script grenepool.py which is awared of output files and, if the run failed, would start from the last keystone intermediate file unless forced.
git clone https://github.com/MoisesExpositoAlonso/grenepool
cd grenepool
make
# to prompt help from the two main programs
./grenepool
./pool
./grenepool.py <yourfile.fastq.gz>
./pool <outputname> <file1.freq> <file2.freq> ...
Probabilistic model to get frequency and estimate changes in time. Two previous softares options might be CLEAR or PoPoolation.