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

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

  -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_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_vcf_filename_prefix        :specify the prefix of the output vcf file