File: vcfmultiway

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libvcflib 1.0.0~rc2%2Bdfsg-2
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#!/bin/bash

reference=$1
shift

echo comparing $@

for fileA in $@;
do
    for fileB in $@;
    do
	if [ "$fileA" = "$fileB" ]
	then
	    vcfstats $fileA >$(basename $fileA).stats.txt
	else
	    vcfintersect -r $reference -i $fileA $fileB | vcfstats >$(basename $fileA).common.$(basename $fileB).stats.txt
	    vcfintersect -r $reference -v -i $fileB $fileA | vcfstats >$(basename $fileA).unique.$(basename $fileB).stats.txt
	fi
    done
done