Custom peak caller for CUT&TAG data relies heavily on the Regulatory Genomics Toolbox API.
Clone this repository, or download the file wget https://raw.githubusercontent.com/maxsonBraunLab/callpeaks/master/callpeaks.py. Then set up dependencies using conda.
# create a conda environment from the environment file
cd callpeaks
conda env create -f callpeaks-env.yml
conda activate callpeaks-env
python callpeaks.py -h
usage: callpeaks.py [-h] -b BAM -o OUTFILE [-cf CONTROLFILE] -cs CHROMSIZES
[-minreads MINREADS] [-minsize MINSIZE] [-pv PVALUE]
[-bs BINSIZE] [-cp CORRECT_PVAL]
Call peaks on CUTTAG bam files
optional arguments:
-h, --help show this help message and exit
-b BAM, --bam BAM Bam file
-o OUTFILE, --outfile OUTFILE
Output prefix (filename without extension)
-cf CONTROLFILE, --controlfile CONTROLFILE
control file for experiment or sample
-cs CHROMSIZES, --chromsizes CHROMSIZES
Genome chromsizes file
-minreads MINREADS, --minreads MINREADS
Minimum number of reads
-minsize MINSIZE, --minsize MINSIZE
Only output peaks greater than or equal to -min-size
-pv PVALUE, --pvalue PVALUE
Pvalue threshold for binomial peak test (default 0.05)
-bs BINSIZE, --binsize BINSIZE
Binsize for output bigwig file (default 100)
-cp CORRECT_PVAL, --correct-pval CORRECT_PVAL
Correct p-values for multiple testing using
Benjamini/Hochberg ("bh") or Benjamini/Yekutieli
("by") method