SRR3221859 130603_D00222_0039_AH0GUHADXX_2_ID06 ARBRMR.FHS-MRI-17313-1_1AMP-23 1 NIL bwa 0.6.2 bwa aln $aln_params -t $t $index_base read.txt > read.sai (repeated for the pair) 2 1 bwa 0.6.2 bwa sampe $sampe_params $index_base read1.sai read2.sai 3 2 picard 1.88 java -jar FixMateInformation.jar I=merge.bam O=fix.bam 4 3 picard 1.88 java –jar MarkDuplicates.jar I=fix.bam METRICS_FILE=metrics.txt O=dedup.bam 5 4 picard 1.88 $java -jar AddOrReplaceReadGroups.jar $rg I=/dev/stdin O=input-$i.bam VALIDATION_STRINGENCY=SILENT 6 5 GATk 2.5-2-gf57256b $java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -I dedup.bam -R ref.fa -nt $nt $known_indels --downsampling_type NONE -o target.intervals 7 6 GATk 2.5-2-gf57256b $java -jar GenomeAnalysisTK.jar -T IndelRealigner -I dedup.bam -R ref.fa -targetIntervals target.intervals -o realigned.bam $known_indels --downsampling_type NONE 8 7 GATk 2.5-2-gf57256b $java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -I realigned.bam -R ref.fa -nct $nt $dbsnps $indels --downsampling_type NONE -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o recal_data.grp 9 8 GATk 2.5-2-gf57256b $java -jar GenomeAnalysisTK.jar -T PrintReads -BQSR recal_data.grp -R ref.fa -I realigned.bam -nct $nt --downsampling_type NONE --emit_original_quals -o recaled.bam