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 (arda.soylev@hhu.de)

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.

asylvz / SVarp