VAriation with LOng Range information

This repository includes code for VALOR2. The original version 1 is deprecated but also available in the rasekh-etal directory for archival purposes.

Citation

VALOR2: characterization of large-scale structural variants using linked-reads. 
Fatih Karaoglanoglu, Camir Ricketts, Ezgi Ebren, Marzieh Eslami Rasekh,
Iman Hajirasouliha, Can Alkan. Genome Biology, 21 (1): 72, 2020.

Requirements

• gcc > 5.4
• zlib (http://www.zlib.net)
• htslib (included; http://htslib.org/)
• sonic (included; https://github.com/calkan/sonic)

How to install VALOR from source

git clone https://github.com/BilkentCompGen/valor.git --recursive
cd valor
make libs
make
cp valor /path/to/your/favorite/binaries

Running VALOR

Required Parameters:

-i, --input [BAM files]        : Input files in sorted BAM format.

-o, --out   [output prefix]    : Prefix for the output files
    
-s, --sonic  [sonic file]      : Sonic file. Check: https://github.com/calkan/sonic.
    
-f, --svs_to_find   [sv type]  : Comma separated list of SVs (i.e. INV,DUP,IDUP,TRA,ITRA,DEL)

Optional Parameters:

-l, --log_file [logfile name]: default is [output prefix]-valor.log
-t, --threads [thread count]: sets number of threads to be used (default is 1)
-p, --ploidy  [Number of chromosome sets]      : Default is 2
-y, --single-copy-chr  [Chromosome name]      : sets copy number of a chromosome to 1 (example -y X -y Y for male humans).	

Help Parameters:

-v, --version                  : Print version and exit.
    
-h, --help                     : Print help screen and exit.

Example:

valor -i input.bam -s hg19.sonic -o output_prefix -f DUP,IDUP,DEL

SONIC file (annotations container)

SONIC files are available under https://github.com/BilkentCompGen/sonic-prebuilt/

• human_g1k_v37.sonic: SONIC file for Human Reference Genome GRCh37 (1000 Genomes Project version)

• ucsc_hg19.sonic: SONIC file for the human reference genome, UCSC version build hg19.

• GRCh38.sonic: SONIC file for the human reference genome build 38.

Make sure that the same reference was used to align the reads beforehand (BAM file) and to create the SONIC file. The SONIC files and the reference FASTA files linked above are compatible.

Building a new SONIC file

Please refer to the SONIC development repository: https://github.com/calkan/sonic/

OUTPUT FORMAT

in [output prefix]-predicted_inversions.bedpe

Chromosome-name BP1-start BP1-end Chromosome-name BP2-start BP2-end SV_TYPE 10XG-Support Read_Pair_Support Molecule_Depth

• Read pair Support: Number of read-pairs that support these breakpoints
• 10XG Support: Number of 10XG Molecule-pairs that support these breakpoints

BEDPE format table

chr1	start1	end1	chr2	start2	end2	type	Support info
chr	bp1-start	bp1-end	chr	bp2-start	bp-end	inversion	...
chr	molecule-start	start	chr	end	molecule-end	deletion
chr	source-start	source-end	chr	target-start	target-end	duplication
source-chr	source-start	source-end	target-chr	target-start	target-end	translocation

Docker Usage

To build a valor Docker image

cd docker
docker build . -t valor:latest

Your image named "valor" should be ready. You can run valor using this image by

docker run --user=$UID -v /path/to/inputs:/input -v /path/to/outputdir:/output valor [args]

• [args] are usual arguments you would pass to valor executable. Be careful about mapping. You need to specify folders respective to container directory structure.
• You need to map host machine input and output directory to responding volume directories inside the container. These options are specified by '-v' argment.
• Docker works with root user by default. "--user" option saves your outputs.