ScanITD

Introduction

ScanITD: detecting internal tandem duplication with robust variant allele frequency estimation

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

You need Python 3.4 and later to run ScanITD.

install necessary python packages via anaconda

Install anaconda (python 3.7) firstly, then install dependent packages via conda in bioconda channel.

conda install -c bioconda pysam
conda install -c conda-forge scikit-bio
conda install -c anaconda numpy
conda install -c bioconda samtools  ## samtools/1.0 or newer is required

Usage

ScanITD.py -i input_bam_file -r indexed_refenence_genome_fasta -o output_vcf_filename_prefix [opts]

Options:

  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        BWA-MEM BAM file
  -r REF, --ref REF     reference genome in FASTA format
  -o OUTPUT, --output OUTPUT
                        output prefix
  -m MAPQ, --mapq MAPQ  minimal MAPQ in BAM for calling ITD (default: 15)
  -c AO, --ao AO        minimal observation count for ITD (default: 4)
  -d DP, --depth DP     minimal depth to call ITD (default: 10)
  -f VAF, --vaf VAF     minimal variant allele frequency (default: 0.1)
  -l ITD_LEN, --len ITD_LEN
                        minimal ITD length to report (default: 10)
  -n MISMATCH           maximum allowed mismatch bases of pairwise local
                        alignment (default: 3)
  -t TARGET, --target TARGET
                        Limit analysis to targets listed in the BED-format
                        file or a samtools region string
  -k, --keep            Kepp the ITD build BAM file
  -v, --version         show program's version number and exit

Input:

input_bam_file                    :input WES BAM file. (e.g., wes-seq.bam)
indexed_reference_genome_fasta    :specify reference genome in FASTA format (the reference genome should be indexed)

Output:

output_vcf_filename_prefix        :specify the prefix of the output vcf file 

The name of the output VCF file will be prefix.itd.vcf.

The Test directory contains files and scripts for testing the installation.

License

This project is licensed under MIT.

Contact

Bug reports or feature requests can be submitted on the ScanITD Github page.

Citation

Wang TY. and Yang R. ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation.