A software to detect structural variations in human genomes by read extension, spliced alignment and local assembly.
Author: Peng Xu
Email: peng.xu@mssm.edu
Draft date: June. 4, 2019
ClipSV was developed to detect structural variations by read extension, spliced alignment and local assembly. It primarily depends on clipped reads from short-read sequencing platform. ClipSV was optimized to discover INDELS (5bp-50bp) and structural variations (>=50bp) in human genomes.
The program was tested on a x86_64 Linux system with 12 cores, each with a 4GB physical memory. The work can be usually finished within 6 hours per 30x whole genome sequencing sample.
Dependency: Python3, samtools (https://github.com/samtools/samtools), minimap2 (https://github.com/lh3/minimap2), bedtools (https://bedtools.readthedocs.io/en/latest/), velvet(https://www.ebi.ac.uk/~zerbino/velvet/) should be installed in current path.
git clone https://github.com/penguab/ClipSV.git
Then, please also add this directory to your PATH:
export PATH=$PWD/ClipSV/:$PATH
ClipSV needs two files as inputs. The first is an indexed bam/cram file from whole genome sequencing. The second is the genome reference indexed by minimap2 (To generate index file, use command "minimap2 -d genome.mmi genome.fa").
For human studies, the latest genome with decoy and HLA cotigs is recommended: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa.
Quick start:
source activate python3
PATH=$PWD/ClipSV/:$PATH
clipsv.py -t 12 -b bam/cram -g genome.fa
Parameters:
clipsv.py -b <bam/cram file> -g <genome.fa> [-dtphv]
-b Indexed bam/cram file
-g Fasta file of genome sequence (Should be indexed by Minimap2 "minimap2 -d genome.mmi genome.fa")
----Optional---
-t Threads (default: 12)
-d Sequencing depth (default: automatically determined)
-p Prefix (default: ClipSV_out)
-v Version
-h Help
6/4/2019: First version released.