multivcf2fasta.sh

## Script to turn a multivcf into a multifasta
## USAGE: bash multivcf2fasta.sh <vcf> <ref> <gatk-style interval string (single locus)> # <outname>
## Started 14 October 2015
## Christian Parobek

## Define useful variables
gatk=/nas02/apps/biojars-1.0/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar
vcf=$1
ref=$2
interval=$3
#outname=$4
time=`date +"%F_%T"`

## make folder for the files
mkdir "multivcfs_$time"

## run a for loop for each individual in the vcf
for name in `grep "CHROM" $vcf | cut -d$'\t' -f10-`
do 

## SPLIT VCF INTO INDIVIDUAL VCFs
java -Xmx2g -jar $gatk \
	-T SelectVariants \
	--variant $vcf \
	-R $ref \
	-sn $name \
	-o multivcfs_$time/$name.tmp.vcf


### REMOVE ALL NON-ENTRIES IN INDIVIDUAL FILES (PL=0 & GT=0)
grep -vP "PL\t0" multivcfs_$time/$name.tmp.vcf | grep -vP "\tGT\t." > multivcfs_$time/$name.vcf

rm multivcfs_$time/$name.tmp.vcf* # remove the files with the extra entries


##for interval in `ls $interval`
##do
	
## VCF TO FASTA
java -Xmx2g -jar $gatk \
	-T FastaAlternateReferenceMaker \
	-R $ref \
	--variant multivcfs_$time/$name.vcf \
	-o multivcfs_$time/$name.fa
	#-L $interval \
	#-o multivcfs_$time/$name$interval.fa
		#--rawOnelineSeq prints only sequence

	echo ">"$name >> multivcfs_$time/$interval.fa
	#grep -v ">" multivcfs_$time/$name$interval.fa >> multivcfs_$time/$interval.fa
	grep -v ">" multivcfs_$time/$name.fa >> multivcfs_$time/$interval.fa
	rm multivcfs_$time/$name.fa

##done

rm multivcfs_$time/*vcf*

done