Merge VCFs

vcfmerge.sh

#!/bin/bash

#Usage: ./vcfmerge.sh {PATH FOR VCFs} a/b/c/

PICARDPATH=/usr/local/bin

STR=""
for f in ${1}*.dv.vcf.gz
do
        if [[ $f != *.dv_merged.vcf.gz ]]
        then
                STR="${STR} INPUT=${f}"
        fi
done

echo "java -jar $PICARDPATH/picard.jar MergeVcfs INPUT=$STR OUTPUT=${1}.dv_merged.vcf" 

java -jar $PICARDPATH/picard.jar MergeVcfs $STR OUTPUT=${1}query.dv_merged.vcf.gz

##################################################################################
'''
STR=""
for f in ${1}*.haplotagged.vcf.gz
do
        if [[ $f != *.haplotagged_merged.vcf.gz ]]
        then
                STR="${STR} INPUT=${f}"
        fi
done

echo "java -jar $PICARDPATH/picard.jar MergeVcfs INPUT=$STR OUTPUT=${1}.haplotagged_merged.vcf" 

java -jar $PICARDPATH/picard.jar MergeVcfs $STR OUTPUT=${1}query.haplotagged_merged.vcf.gz
'''