#!/bin/bash

REF=/scratch/user/u.gz28467/input_files/TAIR10_chr_all.fasta

TDR_BAM=TDr-7_10M_pb.bam

# Number of threads for GATK to use
OMP_NUM_THREADS=8

function haplo_se {
	REF=$1; BAM=$2; PREFIX=$3
	gatk HaplotypeCaller \
		--java-options -Xmx30g \
		--input $BAM \
		--output ${PREFIX}_cpu.vcf \
		--reference ${REF} \
		--native-pair-hmm-threads 16
}

# Call variants on TDr-7 bam file
time haplo_se $REF $TDR_BAM TDr-7_10M