surpyvor

A python wrapper around SURVIVOR, with additional convenience functions.

Installation and dependencies

surpyvor requires bcftools, bgzip, tabix and SURVIVOR to be installed and in the $PATH. Required python modules are cyvcf2, matplotlib, numpy, matplotlib-venn and upsetplot

surpyvor and its dependencies can be installed from bioconda:

conda install -c bioconda surpyvor

USAGE

sub-commands:

merge               merging vcf files of SVs
highsens            get union of SV vcfs
highconf            get intersection of SV vcfs
prf                 calculate precision, recall and F-measure
upset               Make upset plot for multiple SV vcf files
venn                Make venn diagram for 2 or 3 SV vcf files

Each sub-command has its own help information, accessible by running surpyvor <command> -h/--help

General and common arguments for most sub-commands:

-o/--output: output variant file to write. Default: stdout
--plotout: name ouf output plot to write. Default names depending on plot type.
-d/--distance: maximal pairwise distance between coordinates of SVs to be considered concordant. Default: 500
-l/--minlength: minimal SV length to include. Default: 50
--variants: vcf files to combine

Specific arguments

surpyvor prf

--ignore_chroms: ignore some chromosomes for calculations. Default: chrEBV
--bar: create a stacked bar chart colored by validation status [not created by default]
--matrix: create a confusion matrix [not created by default]

Citation

If you use this tool, please consider citing our publication and the citation for SURVIVOR.