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.
