Manipulate vcf files of structural variants using SURVIVOR
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
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
--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]
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