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#!/bin/bash
# overlay files using QUAL and GT from a second VCF
if [ $# -ne 5 ];
then
echo usage: $0 '[ref_fasta] [base_vcf] [extension_vcf] [qual_info_name] [work_dir]'
echo overlays the files, using the QUAL and GT from the extension
exit
fi
ref=$1
base_vcf=$2
extend_vcf=$3
qual_info_name=$4
work=$5
mkdir -p $work
aux_vcf=$work/$(basename $extend_vcf .vcf.gz).aug.vcf.gz
vcfqual2info $qual_info_name $extend_vcf \
| vcfkeepinfo - $qual_info_name \
| vcfkeepgeno - GT \
| vcfallelicprimitives -kg \
| vt normalize -r $ref -q - 2>/dev/null \
| bgziptabix $aux_vcf
echo '##fileformat=VCFv4.1'
sort -r \
<(zcat $base_vcf | head -1000 | grep "^#" | grep -v '^##fileformat') \
<(zcat $aux_vcf | head -1000 | grep "^#" | grep OLD_VARIANT ) \
<(zcat $aux_vcf | head -1000 | grep "^#" | grep $qual_info_name )
vcfintersect -r $ref \
-u <(zcat $base_vcf \
| vcfallelicprimitives -kg \
| vt normalize -r $ref -q - 2>/dev/null ) \
$aux_vcf \
| vcfaddinfo - $aux_vcf \
| vcfstreamsort -w 10000000000 \
| vcfuniq \
| vcfgeno2haplo -r $ref -w 0 \
| vcffixup - \
| grep -v "^#"
rm -f $aux_vcf*
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