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Variant_calling/03.Sf.mapping.Surjeet.sh

+#!/bin/bash
+
+#SBATCH --partition=dgimi-eha
+#SBATCH --mem=5G
+
+
+cd /lustre/durandk/NCBI_ZEA/VariantCalling/
+
+
+
+#/nfs/work/faw_adaptation/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 -x /lustre/durandk/HELICOVERPA/ref_HZEA/GCF_022581195.2_ilHelZeax1.1_genomic  -1 /lustre/durandk/NCBI_ZEA/FQ_Trim/$1".pair1.truncated.gz" -2 /lustre/durandk/NCBI_ZEA/FQ_Trim/$1".pair2.truncated.gz" --very-sensitive-local  | /nfs/work/faw_adaptation/programs/samtools-1.9/samtools view -F 4 -b -h -o /lustre/durandk/NCBI_ZEA/$1".raw.bam"
+
+
+
+#/nfs/work/faw_adaptation/programs/samtools-1.9/samtools sort -o $1".sorted.bam" $1".raw.bam"
+
+#rm SAMPLE.raw.bam
+
+module load JDK/jdk.8_x64
+#java -Xmx4g -Djava.io.tmpdir=temp.SAMPLE -jar  /nfs/work/faw_adaptation/programs/picard.jar MarkDuplicates INPUT=$1".sorted.bam" OUTPUT=$1".dupl_rm.bam" REMOVE_DUPLICATES=true METRICS_FILE=$1".metricN.log" ASSUME_SORTED=True MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000
+
+#rm -rf temp.SAMPLE
+#rm SAMPLE.sorted.bam
+
+#java -Xmx4g -Djava.io.tmpdir=$1".SAMPLE" -jar /nfs/work/faw_adaptation/programs/picard.jar AddOrReplaceReadGroups INPUT=$1".dupl_rm.bam" OUTPUT=$1".bam" RGID=$1 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=$1;
+
+#rm -rf temp.SAMPLE
+#rm SAMPLE.dupl_rm.bam
+
+/nfs/work/faw_adaptation/programs/samtools-1.9/samtools index $1".bam"   
+/nfs/work/faw_adaptation/programs/samtools-1.9/samtools stats $1".bam" > $1".stats"