vcfjoincalls

#!/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*