https://github.com/asylvz/SVarp

Phased structural variant discovery in pangenomes
https://github.com/asylvz/SVarp

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Phased structural variant discovery in pangenomes

• Host: GitHub
• URL: https://github.com/asylvz/SVarp
• Owner: asylvz
• License: mit
• Created: 2022-12-31T22:43:14.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2024-05-31T11:32:54.000Z (5 months ago)
• Last Synced: 2024-06-12T05:35:37.186Z (5 months ago)
• Language: C++
• Homepage:
• Size: 307 KB
• Stars: 24
• Watchers: 1
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-pangenomes - SVarp

README

        
# SVarp 

***Pangenome-based structural variant discovery***

The aim of SVarp is to discover haplotype resolved SVs on top of a pangenome graph reference using long sequencing reads. It outputs local assemblies of SV alleles, termed *svtigs*.

*Please open an issue for your questions or feel free to send me an e-mail ([email protected])*

## Quick Start

	git clone https://github.com/asylvz/SVarp.git

	cd svarp

	make

	build/svarp -a xxx.gaf -g xxx.gfa --fasta xxx.fasta.gz --phase read_tags.tsv -i SAMPLE_NAME -o OUTPUT_FOLDER

## Requirements

SVarp is developed and tested using Linux Ubuntu operating system

* You need the FASTA of the reads **bgzipped** (i.e., bgzip NA12878.fasta)

* GAF file needs to be in **unstable coordinate system**. (https://github.com/lh3/gfatools/blob/master/doc/rGFA.md)

* Pangenome ref. needs to be in GFA format. We tested SVarp with **HPRC Minigraph pangenome** (https://zenodo.org/record/6983934)

	- GAF alignments must be generated using the same GFA file that you use as input

* For **phased variants**, tags need to be generated in ".tsv" format using **whatshap haplotag** (https://whatshap.readthedocs.io/)

	- E.g., *whatshap haplotag NA12878.vcf.gz NA12878.bam -o NA12878_phase --reference ref_genome.fasta --output-haplotag-list tags.tsv*

## Dependencies

* **wtdbg2** 

 	- git clone https://github.com/ruanjue/wtdbg2 && cd wtdbg2 && make (copy *wtdbg2*, *wtpoa-cns* and *wtdbg2.pl* to your PATH)

* **zlib**

  	- sudo apt-get install zlib1g-d

* **GraphAligner**

  	- conda install -c bioconda graphaligner (https://github.com/maickrau/GraphAligner)

* **Samtools**

  	- https://github.com/samtools/samtools

* **Minimap2**

  	- git clone https://github.com/lh3/minimap2 && cd minimap2 && make

* **HTSlib and WFA2-lib**

  	- You can either use ***make libs*** or follow the steps below

### HTSlib (https://github.com/samtools/htslib)

	wget https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2

	mkdir htslib && tar -xvf htslib-1.17.tar.bz2 -C htslib --strip-components=1

	cd htslib && autoconf -i && ./configure --disable-lzma --disable-bz2 --disable-libcurl && make

	(htslib folder needs to reside inside SVarp's main folder)

### WFA2-lib (https://github.com/smarco/WFA2-lib)

	wget https://github.com/smarco/WFA2-lib/archive/refs/tags/v2.3.4.tar.gz --strip-components=1

	mkdir wfa && tar -xzf v2.3.4.tar.gz -C wfa

	cd wfa && make clean all

	(wfa folder needs to reside inside SVarp's main folder)

## All parameters

	Required arguments:

	--gaf (-a)                  : Alignment file in GAF format

	--graph (-g)                : Pangenome file in GFA format

	--fasta (-f)                : Fasta sequence file

	Optional arguments:

	--sample (-i)               : Sample name.

	--out (-o)                  : Output folder.

	--debug                     : Output multiple log files for debugging purpose.

	--skip-untagged             : Output only phased variants (~30% faster).

	--dist_threshold (-d)       : Distance threshold to merge SV breakpoints (default=100)

	--out (-o)                  : Output folder path

	--phase (-p)                : WhatsHap haplotag file in .tsv (https://whatshap.readthedocs.io/en/latest/guide.html#whatshap-haplotag)

	--reads(-r)                 : Bgzipped FASTA file of reads for extensive mode (needed for WFA realignment)

	--sample (-i)               : Sample (Individual) name

	--support (-s)              : Minimum support for a cluster to be assembled (default=5 for diploid samples)

	--threads(-t)               : Number of threads for assembly and realignment (default:32)

	--help                      : Print this help menu

## Citation

*Soylev, A., Ebler, J., Pani, S., Rausch, T., Korbel, J., & Marschall, T. (2024). **SVarp: pangenome-based structural variant discovery**. bioRxiv, 2024-02.*