inScan is devoloping for finding genomic insertion variation from long reads(from both Pacbio and Nanopore sequencing). inScan differs from the published state of art Structure Variation detecting tools(Sniffles and NanoSV) for long reads sequencing technology in two ways. First, inScan can find complex insertions when the insert sequence mapped to another chromosome. Second, inScan detects insertions in a given region, therefore useful for quickly checking if there are insertions in the region(Short Tandem Repeat region for example) of interest.
Python3.6.2 or later
- pysam
git clone git@github.com:Nextomics/inScan.git
cd inScan
python3 inScan.py input.bam input.bed output.jsoninScan takes three positional arguments, a bam file, a bed file, a output file name.
inScan has been tested using NGMLR, BWA mem, Minimap2 output bam files. Generally, inScan will work for a bam file with "SA" tag.
bed file contains the regions to be tested.
output json: {"region":{"reads":[["chromosome","start","end","insert_size"],...],...},...}