This is a toolkit to perform population based filtering of variants called from NGS data
- python2.7
- tqdm (python module; install using
pip install tqdm)
git clone --recursive https://github.com/jodyphelan/variantDetection.git
cd variantDetection/
bash install_prerequisites.sh
To run the pipeline you will need VCFs and a special pileup file (created using htsbox). They should be deposited in folders named fastq and pileup.
The final structure will look like the following:
base_dir/
├──pileup/
│ ├──sample1_1.pileup.gz
│ └──sample1_1.pileup.gz.tbi
└──vcf/
└──sample1.vcf.gz
Two variables are set to call alleles:
- The minimum read depth to call alleles at
- The minimum proportion of reads at a position with an allele
To run the pipeline run the command:
python /path/to/filter_variants.py raw <samples> <base_dir> <min_depth> <read_prop>
python /path/to/filter_variants/py filter