SRR1040585 0710_20101124_1_SP_ANG_MID00558_MID_sA_01003380682_1_BC2 FHSEB.BFR4490-1_1AMP_1 1 NIL bwa 0.5.9 bwa aln reference.fasta 1.fastq > fastq.sai (repeated for the pair) 2 1 bwa 0.5.9 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 1.51 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 2.5-2-gf57256b 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 2.5-2-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 8 7 GATk 2.5-2-gf57256b 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 2.5-2-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 10 9 picard 1.41 java -jar MergeSamFiles.jar I=barcode_recal.realigned-1.bam I=barcode_recal.realigned-2.bam I(x)=barcode_recal.realigned-x.bam O=sample.merged.bam 11 10 picard 1.41 java -jar MarkDuplicates.jar I=sample.merged.bam METRICS_FILE=metric_file.picard O=sample.dups.bam 12 11 samtools 0.1.7(r510) samtools index sample.dups.bam 13 12 GATk 2.5-2-gf57256b java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -I sample.dups.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 sample.intervals 14 13 GATk 2.5-2-gf57256b java -jar GenomeAnalysisTK.jar -T IndelRealigner -I sample.dups.bam -R reference.fasta -targetIntervals sample.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 sample_realigned.bam 15 14 GATk 2.5-2-gf57256b java -jar GenomeAnalysisTK.jar -T BaseRecalibrator I=sample_realigned.bam -R reference.fasta -o sample.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 sample.csv 16 15 GATk 2.5-2-gf57256b java -jar GenomeAnalysisTK.jar -T PrintReads -I sample_realigned.bam -R reference.fasta -BQSR sample.GATKrecal_data.grp --emit_original_quals --downsampling_type NONE -o sample_recal.realigned.bam 17 16 samtools 0.1.7(r510) samtools calmd -b sample_recal.realigned.bam reference.fasta > sample_recal.realigned.calmd.bam 18 17 picard 1.84 java -jar ValidateSamFile.jar I=sample_recal.realigned_calmd.bam O=validation.results reference.fasta