Padfoot is a structural variant (SV) and copy number alteration (CNA) annotation tool designed to work seamlessly with output from Severus and Wakhan. It provides biological and functional annotations for SVs and CNAs, enabling downstream interpretation of genomic alterations.
- Annotates somatic SVs called by Severus
- Annotates CNAs reported by Wakhan
- Outputs functional annotations for prioritization
- Designed for cancer genome analysis using long-read data
The easiest way to install is through conda:
conda create -n padfoot_env padfoot
conda activate padfoot_env
padfoot --help
Or alternatively, you can clone the repository and run without installation, but you'll still need to install the dependencies via conda:
git clone https://github.com/KolmogorovLab/Padfoot.git
cd Padfoot
conda env create --name padfoot_env --file environment.yml
conda activate padfoot_env
./padfoot.py
padfoot --severus-vcf severus_somatic.vcf --wakhan-vcf wakhan_cna.vcf --ref ref.fa --out-dir padfoot_out -t 16 --specie human
--severus-vcf path to Severus vcf
--wakhan-vcf path to Wakhan vcf
--ref path to reference fasta file (needs to be indexed)
--out-dir path to output directory
--threads number of threads [8]
--specie human or mouse or user defined(GFF and rm files need to be provided) [human]
--genome Either hg38, chm13 or mm10 [hg38]
--gff If user want to use a alternative gff
--rm Repeat masker file (.fa.out)
We provide default GFF and RepeatMasker annotation files in the bed/ directory.
If you would like to use a different genome assembly or custom annotations, you can specify your own files using the following parameters:
--gff: Path to a custom GFF annotation file--rm: Path to a custom RepeatMasker BED file--specie: Specify the species or genome build (e.g.,hg38,chm13)
These options allow flexibility for applying Padfoot to a variety of genome references and annotation sources.
The output is a tab-delimited file containing:
- Annotated SVs and CNAs
- Gene overlaps and exon-level effects
- Functional impact scores
- Complex SV plots
Padfoot is distributed under a BSD license. See the LICENSE file for details.
Padfoot was developed by the Kolmogorov Lab at the National Cancer Institute as part of ongoing efforts to improve interpretation of long-read somatic variant data in cancer genomics.
Key contributors:
- Ayse Keskus
- Mikhail Kolmogorov
For advising, bug reporting and requiring help, please submit an issue. You can also contact the developer: aysegokce.keskus@nih.gov