1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
|
#!/bin/bash
reference=$1
outdir=$2
scriptsdir=$3
shift
shift
shift
mkdir -p $outdir
mkdir -p $scriptsdir
echo comparing $@
for fileA in $@;
do
fileA=$(pwd)/$fileA
for fileB in $@;
do
fileB=$(pwd)/$fileB
echo $fileA vs $fileB
if [ "$fileA" = "$fileB" ]
then
echo "vcfstats $fileA >$outdir/$(basename $fileA).stats" >$scriptsdir/$(basename $fileA).sh
else
echo "vcfintersect -r $reference -i $fileA $fileB | vcfstats >$outdir/$(basename $fileA).common.$(basename $fileB).stats" >$scriptsdir/$(basename $fileA).common.$(basename $fileB).sh
echo "vcfintersect -r $reference -v -i $fileB $fileA | vcfstats >$outdir/$(basename $fileA).unique.$(basename $fileB).stats" >$scriptsdir/$(basename $fileA).unique.$(basename $fileB).sh
fi
done
done
|
