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Commit 3746c07f authored by Brandi Cantarel's avatar Brandi Cantarel
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update abra

parent ec7b3630
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......@@ -17,7 +17,7 @@ do
r) index_path=$OPTARG;;
b) sbam=$OPTARG;;
p) pair_id=$OPTARG;;
c) tbed==$OPTARG;;
c) tbed=$OPTARG;;
h) usage;;
esac
done
......@@ -54,5 +54,5 @@ fi
which samtools
samtools index -@ $NPROC ${sbam}
mkdir tmpdir
java -Xmx16G -jar ${abrajar} ${ioopt} --ref ${index_path}/genome.fa --threads $NRPOC $opt --tmpdir tmpdir --mbq 150 --mnf 5 --mer 0.05 > abra.log
java -Xmx16G -jar ${abrajar} ${ioopt} --ref ${index_path}/genome.fa --threads $NPROC $opt --tmpdir tmpdir --mbq 150 --mnf 5 --mer 0.05 > abra.log
samtools index -@ $NPROC ${pair_id}.abra2.bam
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