emauryg / cnv_mips

Call CNVs from MIPS data

This is a wrapper on the cnvkit software https://github.com/etal/cnvkit.

To install follow the instructions below from the cnvkit github

Using Conda

# 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

Using pip

pip install cnvkit

Please read their github for other R and python dependencies.

Get the RefFlat file containing a gene annotation

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.

Running the cnv calling with mips data

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.