SRR1724514 130222_SN1133_0278_BH0C72ADXX_2_ID01 BRSTCA.7036-PT13-N-1_1AMP_1 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 3 2 MateInfoFixer 1.0 java -jar MateInfoFixer.jar I=barcode.sam O=barcode.sorted.bam 4 3 picard 1.84 java -jar MarkDuplicates.jar I=barcode.sorted.bam O=barcode.marked.bam 5 4 samtools 0.1.7(r510) samtools index barcode.marked.bam 6 5 GATk 2.3-9-ge5ebf34 java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -I barcode.marked.bam -R reference.fasta -nt 8 --downsampling_type NONE -known 1000G_phase1.indels.b37.vcf.gz -known Mills_and_1000G_gold_standard.indels.b37.vcf.gz -o barcode.intervals 7 6 GATk 2.3-9-ge5ebf34 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 8 7 GATk 2.3-9-ge5ebf34 java -jar GenomeAnalysisTK.jar -T BaseRecalibrator I=barcode_realigned.bam -R reference.fasta -o barcode.GATKrecal_data.grp --downsampling_type NONE -knownSites dbsnp_137.b37.vcf.gz -knownSites 1000G_phase1.indels.b37.vcf.gz -knownSites Mills_and_1000G_gold_standard.indels.b37.vcf.gz -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate-dP illumina -knownSites:dbSNP,VCF sites.vcf.gz -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile barcode.csv 9 8 GATk 2.3-9-ge5ebf34 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 10 9 picard 1.84 java -jar ValidateSamFile.jar I=barcode_recal.realigned_calmd.bam O=validation.results reference.fasta