SRR3082797 140722_SN898_0576_BC4GF8ACXX_1_ID03 PAMPC3.TUD-CC-757-N-1_1AMP-6 1 NIL bwa 0.6.2 bwa aln reference.fasta 1.fastq > fastq.sai (repeated for the pair) 2 1 bwa 0.6.2 bwa sampe reference.fasta fastq1.sai fastq2.sai > barcode.sam 4 3 picard 1.93 java -jar MarkDuplicates.jar I=barcode.sorted.bam O=barcode.marked.bam 7 6 GATk 2.5-2-gf57256b java -jar GenomeAnalysisTK.jar -T IndelRealigner -I barcode.marked.bam -R reference.fasta -targetIntervals barcode.intervals --downsampling_type NONE --consensusDeterminationModel USE_READS -known 1000G_phase1.indels.b37.vcf.gz -known Mills_and_1000G_gold_standard.indels.b37.vcf.gz -o barcode_realigned.bam 9 8 GATk 2.5-2-gf57256b java -jar GenomeAnalysisTK.jar -T PrintReads -I barcode_realigned.bam -R reference.fasta -BQSR barcode.GATKrecal_data.grp --emit_original_quals --downsampling_type NONE -o barcode_recal.realigned.bam