I got a bunch of vcf files (v4.1) with structural variations of bunch of non-model organisms (i.e. there are no known variants). I found there are quite a some tools to manipulate vcf files like VCFtools, R package vcfR or python library PyVCF. However none of them seems to provide a quick summary, something like (preferably categorised by size as well):
type count DEL x INS y INV z ....
Is there any tool or a function I overlooked that produces summaries of this style?
I know that vcf file is just a plain text file and if I will dissect
ALT columns I should be able to write a script that will do the job, but I hoped that I could avoid to write my own parser.
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So far it seems that only tool that aims to do summaries (@gringer answer) is not working on vcf v4.1. Other tools would provide just partial solution by filtering certain variant type. Therefore I accept my own parser perl/R solutions, till there will be a working tool for stats of vcf with structural variants.