added the runBWA script

runBWA.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+module load bwa
+module load samtools
+GENOMEDIR="/work/GIF/arnstrm/GENOMEDB"
+#GNAME="Btau_4.6.1_chromosomes.fa"
+GNAME="$1"
+REF="$GENOMEDIR/$GNAME"
+THREADS="16"
+READ1="$2"
+READ2="$3"
+SAM=$(basename ${READ1%.*} | cut -f 1-2 -d "_")
+bwa mem -M -x ont2d -t ${THREADS} ${REF} ${READ1} ${READ2} > ${SAM}.sam
+samtools view --threads 16 -b -o ${SAM}.bam ${SAM}.sam
+samtools sort -m 8G -o ${SAM}_sorted.bam -T ${SAM}_temp --threads 16 ${SAM}.bam