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Structural Variant Prediction Viewer

SVPV enables visualisation of predicted structural variant regions in paired-end whole genome sequencing alignments, and allows comparison of calls from differenct structural variant prediction algorithms. Statistics related to structural variants are presented in a form that allows users to visually identify false postive calls. Input is a set alignment files (SAM/BAM/CRAM format) along with a set of structural variant predictions on these alignments (VCF files). Output is a set of pdf files of structural variant regions. Please see the wiki for examples of SVPV plots of different structural variant categories.

SVPV supports VCF structural variant types deletion (DEL), duplication (DUP), copy number variation (CNV), inversion (INV), insertion (INS) and breakend ('BND'). Delly2-style translocations (TRA) are also supported.

Requirements

Command Line Mode

  • Python 2.7.+ and NumPy
  • R v3.+
  • SAMtools and BCFtools (version 1.3)
  • Linux environment, or access to linux via ssh

Note: SAMtools and BCFtools must be executable by typing 'samtools' and 'bcftools' into the terminal.

GUI Mode

  • All command line mode requirements, and:
  • X11 if running over ssh
  • python 2.7 tkinter
  • Recommended: GraphicsMagick or ImageMagick ('display')
    • GraphicsMagick build w/ --enable-magick-compat
    • Note: any other X11 capable pdf viewer specified by '-disp' will work
    • alternatively users can navigate to plot directory and open the file with a local pdf viewer

Installation

  • Navigate to desired install directory and clone this repository.

    git clone https://github.com/VCCRI/SVPV.git SVPV

  • Ensure that requirements are met. For convenience shell scripts are provided for Ubuntu and CentOS.

    sudo sh ./SVPV/set_up/Ubuntu_set_up.sh

  • Test that SVPV is working. If you get any error messages at this point it is likely that some requirements aren't met.

    python ./SVPV/SVPV -example

  • Test the gui is working

    python ./SVPV/SVPV -example -gui

  • all done!

Non-linux users

  • The easiest way to get SVPV running on your Windows or Mac is to run a virtual machine in software such as Oracle VM Virtual Box.
  • You can download an Ubuntu 16.04 image at osboxes.org
  • After your Ubuntu image is running follow the installation instructions above

Usage

Running in GUI mode allows users to select and view individual structural variant calls on some subset of the supplied samples. Running in batch mode (i.e. not GUI mode) will generates plots for each call with the suplied set of samples, matching the supplied filter arguments.

Run args: Description Notes
-vcf1 Comma separated list of structural variant prediction VCF/BCF files required
-o Output directory required
-aln Comma separated list of alignment files (indexed BAM/CRAM) required 2
-samples Comma separated list of samples to view, names must be the same as in VCF required 2
-gui run in gui mode optional
-ref_vcf1 Reference structural variant vcf/bcf file for annotation optional
-ref_gene Refseq genes regene table file for annotation3 optional
-manifest Whitespace delimited file, first column sample names,
second column alignment file path. Overrides '-samples' and '-aln' if also given.		 optional
-ped Tab separated pedigree file (GUI only) optional
-fam Restrict to this family id only. Requires '-ped'. optional
-separate_plots Plot each sample separately optional
-l_svs show SVs extending beyond the current plot area. optional
-disp PDF viewer command. GUI mode only. Default: "display" optional
-rd_len sequencing read length, optimises window size. Default: 100 optional
-exp window expansion, proportion of SV len added to each side. Default: 1 optional
-bkpt_win breakpoint window, number of read lengths to set windows around breakpoints
Default:5		 optional
-n_bins target number of bins for plot window. Default: 100 optional

1vcfs may be specified by a file (e.g. '-vcf /path/to/file.vcf') or by a name and a file (e.g. '-vcf delly:/path/to/file'). If not specified names will be 'vcf 1', 'vcf 2', etc and 'reference' by default.

2'-samples' and '-aln' not required if '-manifest' is supplied.

3Availble for a variety of reference genomes at UCSC Table Browser

Filter args: Description Example
-max_len maximum length of structural variants (bp)
-min_len minimum length of structural variants (bp)
-af Allele frequency threshold -af <0.1
-gts Specify genotypes of given samples sample1:0/1,1/1;sample2:1/1
-chrom Restrict to comma separated list of chromosomes
-svtype Restrict to given SV type (DEL/DUP/CNV/INV)
-rgi Restrict to SVs that intersect refGenes,
'-ref_gene' must be supplied
-exonic Restrict to SVs that intersect exons of refGenes,
'-ref_gene' must be supplied
Plot args: Default Description
-d 1 force sequencing depth plot on or off
-or 1 force orphaned reads plot on or off
-v 1 force inverted pairs plot on or off
-ss 1 force same strand pairs plot on or off
-cl 1 force clipped reads plot on or off
-se 0 force SAM 'secondary alignment' plot on or off
-su 0 force SAM 'supplementary alignment' plot on or off
-dm 0 force mate different molecule alignment plot on or off
-i 1 force inferred insert size plot on or off
-r 1 force refgenes plot on or off
-af 1 force allele frequency plot on or off
-l 1 force plot legend on or off

Usage example:

python SVPV -gui -o ./example/output/ -vcf delly:./example/delly.vcf,cnvnator:./example/cnvnator.vcf -manifest
/example/example.manifest -ref_gene ./example/hg38.refgene.partial.txt -ref_vcf 1000G:./example/1000G.vcf

Advance usage example:

python SVPV -vcf caller1_svs.vcf,caller2_svs.vcf -samples sample1,sample2,sample3 -aln s1.bam,s2.bam,s3.bam
-o /out/directory/ -ref_vcf 1000_genomes_svs.vcf -ref_gene hg38.refgene.txt -max_len 100000 -af <0.25 -gts
sample1:1/1,0/1;sample3:0/0 -svtype DEL -exonic -ss 0 -se 1

VCF Field Requirements:

SV Type Required VCF Fields
All Types CHROM, POS, SVTYPE1, GT2
DEL/DUP/CNV/INV SVLEN or END
INS SVLEN or INSLEN*
BND ALT, ID, MATEID/PAIRID/EVENTID
TRA* CHR2, END

1If SVTYPE is not found then ALT is parsed for symbolic alternate alleles. These should match one of DEL, DUP, CNV, INS, INV, BND or TRA or the call will be ignored.

2For reference VCF only, GT is not required if AF is present.

*Included for compatibility with Delly2

Please see the VCF specifications for further details.

SVPV Plot Window Sizing and Types

  • Please see the wiki

Citation

Jacob E. Munro, Sally L. Dunwoodie, Eleni Giannoulatou; SVPV: a structural variant prediction viewer for paired-end sequencing datasets. Bioinformatics 2017; 33 (13): 2032-2033. doi: 10.1093/bioinformatics/btx117