Distance between variants in a VCF. javascript src for bioalcidae https://github.com/lindenb/jvarkit/wiki/BioAlcidae

distance.js

/**

distribution of distance between variants. Non-Variant, Filterer or GVCF blocks are ignored

usage:
 java -jar jvarkit-git/dist/bioalcidae.jar -f distance.js input.vcf | sort -k1,1g | uniq -c


*/
var prev=null;



function distance(ctx)
	{
	if(!ctx.isVariant() || ctx.isFiltered() || (ctx.getAlleles()==2 && ctx.hasAttribute("END") && ctx.getAlternateAlleles().get(0).getDisplayString().equals("<NON_REF>")) ) return;
	if(prev!=null && prev.getContig().equals(ctx.getContig()))
		{
		var d= parseInt(ctx.getStart()-prev.getEnd());
		out.println(d);
		}
	prev=ctx;
	}


while(iter.hasNext()) distance(iter.next());