This is a wrapper on the cnvkit software https://github.com/etal/cnvkit.
To install follow the instructions below from the cnvkit github
# Configure the sources where conda will find packages conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge
conda install cnvkit
pip install cnvkit
Please read their github for other R and python dependencies.
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz
Note that this refFlat file would be in hg19 format, so if your data is in other reference genome, then it might not work.
python cnv_call_mips.py -bam_dir <bam_directory> -fasta_ref <fasta_path> -bait <bed_path> -out_dir <output_directory> -sample_table <table_with_mipID_and_subjectnames> -refFlat <path_refFlat.txt>
In the above script -refFlat
can be left out empty, and is optional.