ScanIndel is a python program to detect indels (insertions and deletions) from NGS data by re-align and de novo assemble soft clipped reads.
Softwares and Python packages:
- BedTools/2.17.0 (https://github.com/arq5x/bedtools2/releases)
- SAMtools/1.0 or less than 1.0 (http://samtools.sourceforge.net/)
- BWA/0.7.10 (http://bio-bwa.sourceforge.net/)
- BLAT (gfServer and gfClient)/34+ (http://genome.ucsc.edu/FAQ/FAQblat.html)
- freebayes/0.9.18 (https://github.com/ekg/freebayes)
- Inchworm assembler (http://inchworm.sourceforge.net)
- Python/2.7 (https://www.python.org/)
- Pysam/0.7.7 (https://code.google.com/p/pysam/)
- PyVCF/0.6.7 (https://github.com/jamescasbon/PyVCF)
- Biopython/1.64 (http://biopython.org/wiki/Main_Page)
- SciPy/0.14.0 and NumPy/1.8.1 (http://www.scipy.org/)
All softwares above are assumed to be installed in your searching path. Ask your admistrator for assistance if necessary.
git clone git://github.com/cauyrd/ScanIndel.git
cd ScanIndel
python ScanIndel.py -i sample.txt -p config.txt [options]
-F :setting min-alternate-fraction for FreeBayes (default 0.2)
-o :setting output directory (default ./)
-C :setting min-alternate-count for FreeBayes (default 2)
-s :softclipping percentage triggering BLAT re-alignment (default 0.2)
-t :setting -t for FreeBayes to provide a BED-format file limiting the analysis to these regions
--min_percent_hq :min percentage of high quality base in soft clipping reads (default 0.8)
--lowqual_cutoff :low quality cutoff value (default 20)
--mapq_cutoff :low mapping quality cutoff (default 1)
--blat_ident_pct_cutoff :Blat sequence identity cutoff (default 0.8)
--gfServer_port :gfServer service port number, changing this value to allow multiple ScanIndel running at a single machine (default 50000)
--hetero_factor :The factor about the indel heterogenirity and heterozygosity (default 0.1)
--bam :the input file is BAM format
--rmdup :exccute duplicate removal step before realignment
-h --help :produce this menu
-v --version :show version of this tool
sample.txt :this file contains the listed samples to be analyzed (one per line), the input can be raw read FastQ file or aligned BAM file and use --bam when running (default name is sample.txt)
config.txt :this file contains the path of reference file for each BWA, BLAT and Freebayes (default name is config.txt)
The output files include the VCF file for detected variant and BAM files for BWA-MEM and BLAT mapping.
*.reads.bam :BAM file for read after blat alignment.
*.contigs.bam :BAM file for de novo assembled contigs after BWA and BLAT mapping.
*.mapping.indel.vcf :VCF file includes putative INDELs from softclipping read re-alignment.
*.assembly.indel.vcf :VCF file includes putative INDELs from de novo assembly.
*.merged.indel.vcf :VCF file that include all putative INDELs by merging the results from *mapping.indel.vcf and *.assembly.indel.vcf
To run a test example, please go to folder 'example' and follow the README file to run test data.
Yang, Rendong, et al. "ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly." Genome medicine 7.1 (2015): 1-12.