ClipCrop

description

This is a tool for detecting structural variations using soft-clipping information From SAM files.

installation

dependencies

ClipCrop uses SHRiMP2 or bwa internally.

First you have to install SHRiMP2 or bwa (>=v0.5) and add the binary to PATH env. If you use SHRiMP2, "export SHRIMP_FOLDER=/path/to/SHRiMP2" to your env.

install ClipCrop

ClipCrop is implemented in Node.js.

For users who are used to Node.js, just

$ npm install clipcrop

Of course, in the field of bioinformatics, Node.js is still not a major scripting language,

You should install Node.js by its version manager called nvm.

Do not install Node.js from apt-get or other OS package managers!

$ git clone git://github.com/creationix/nvm.git ~/.nvm

$ source ~/.nvm/nvm.sh

$ nvm install v0.6.1

$ nvm use v0.6.1

$ npm install clipcrop

The installation of Node.js may take a long time, but be patient.

For later use, it is better to write the following lines to your .bashrc (or alternatives).

source ~/.nvm/nvm.sh
nvm use v0.6.1

usage

$ clipcrop <sam file> <reference fasta file> [<fasta information json file>]

args

sam file	SAM file with soft-clipping information. The recommended mapping tool is [bwa](http://bio-bwa.sourceforge.net/).
reference fasta file	reference genome used for mapping
fasta information json file (optional)	JSON file for [FASTAReader](https://github.com/shinout/FASTAReader). This file optional, and is used for faster reading of reference genomes. See README of FASTAReader for more detail.

options

dir	directory to put result files. default = basename(path)
bp_filter_parallel	the number of processes to use to filter breakpoints. default: 8
max_diff	max difference within breakpoint cluster values. default: 2
min_cluster_size	minimum cluster size to be a valid breakpoint. default: 10
min_quality	minimum base quality score to allow, default: 5
bases_around_break	number of extended bases around breakpoint to be mapped by clipped sequences. default: 1000
sv_max_diff	max difference within breakpoint cluster values. default: 10
sv_min_cluster_size	minimum cluster size to be a valid SV. default: 10
bwa_threads	the number of threads bwa uses. default: 8

results

results are formatted as BED format.

#rname  start end type  subtype len score rname2  start2  caller  other
chr1  224199455 224199456 INS * * 38  = * clipcrop  num:158 LR:49/109

rname	the name of the chromosome
start	start position of the SV events
end	end position of the SV events
type	SV types (one of DEL, INS, INV, CTX, DUP) CTX : translocation
subtype	subtypes of each SV types.
len	length of the event
score	reliability score of the event. If 0, it cannot be reliable.
rname2	(for translocation) the chromosome of the second breakpoint.
start2	(for translocation) the start position of the second breakpoint.
caller	always "clipcrop"
other.num	the number of supported sequences of the breakpoint
other.LR	the number of L/R clips