annotate_gemini_PS

#!/bin/bash

#annotate a gemini DB with the PS field of a VCF

#help output
if [ "$1" == "-h" ]; then
 echo "PLEASE USE ABSOLUTE PATHS!"
 echo "Usage: `basename $0` [vcf to extract PS and annotate] [gemini db to annotate]"
  exit 0
fi

#make sure there is an inputfile
if [ $# -eq 0 ]
  then
    echo "No arguments supplied"
    echo "Use -h for info"
    exit 1
fi



#extract the PS field

echo "-------Extracting PS field------"

vcftools --gzvcf $1 --extract-FORMAT-info PS --stdout > annots1.tab; sed -i '1d' annots1.tab

#print it in .bed format
awk '{print $1,$2,$2,$3,$4}' annots1.tab > annots.tab

sed -i 's/-1/0/g' annots.tab

sed -i 's/ /\t/g' annots.tab

bgzip annots.tab
tabix -s1 -b2 -e3  annots.tab.gz

echo "--------Annotating your VCF----------"

#annotate the VCF
bcftools annotate -a annots.tab.gz -h /mnt/home/stephen/Apps/bin/annots.hdr -c CHROM,FROM,TO,INFO/PS_tag $1 -o temp.vcf

#bgzip and index
bgzip temp.vcf
tabix -p vcf temp.vcf.gz

#perform annotation of the gemini DB

echo "---------Annotating your Gemini DB-----------"

gemini annotate -f temp.vcf.gz -a extract -c phase_set -t integer -e PS_tag -o list $2

echo "--------Cleaning up----------"

rm annots1.tab
rm temp.vcf.gz*