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@RG	ID:D0ENM.7	PL:illumina	PU:D0ENMACXX111207.7.CCAGTTAG	LB:Sage-75643	DT:2011-12-07T00:00:00-0500	SM:HCC1143	CN:BI
@PG	ID:GATK TableRecalibration	VN:1.3-14-g59da26a	CL:default_read_group=null default_platform=null force_read_group=null force_platform=null window_size_nqs=5 homopolymer_nback=7 exception_if_no_tile=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION recal_file=/seq/picard/D0ENMACXX/C1-210_2011-12-07_2011-12-18/1/Sage-75643/D0ENMACXX.1.recal_data.csv preserve_qscores_less_than=5 smoothing=1 max_quality_score=50 doNotWriteOriginalQuals=false no_pg_tag=false fail_with_no_eof_marker=false skipUQUpdate=false Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate]
@PG	ID:GATK TableRecalibration.1	VN:1.3-14-g59da26a	CL:default_read_group=null default_platform=null force_read_group=null force_platform=null window_size_nqs=5 homopolymer_nback=7 exception_if_no_tile=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION recal_file=/seq/picard/D0ENMACXX/C1-210_2011-12-07_2011-12-18/3/Sage-75643/D0ENMACXX.3.recal_data.csv preserve_qscores_less_than=5 smoothing=1 max_quality_score=50 doNotWriteOriginalQuals=false no_pg_tag=false fail_with_no_eof_marker=false skipUQUpdate=false Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate]
@PG	ID:GATK TableRecalibration.2	VN:1.3-14-g59da26a	CL:default_read_group=null default_platform=null force_read_group=null force_platform=null window_size_nqs=5 homopolymer_nback=7 exception_if_no_tile=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION recal_file=/seq/picard/D0ENMACXX/C1-210_2011-12-07_2011-12-18/7/Sage-75643/D0ENMACXX.7.recal_data.csv preserve_qscores_less_than=5 smoothing=1 max_quality_score=50 doNotWriteOriginalQuals=false no_pg_tag=false fail_with_no_eof_marker=false skipUQUpdate=false Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate]
@PG	ID:GATK TableRecalibration.3	VN:1.3-14-g59da26a	CL:default_read_group=null default_platform=null force_read_group=null force_platform=null window_size_nqs=5 homopolymer_nback=7 exception_if_no_tile=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION recal_file=/seq/picard/D0ENMACXX/C1-210_2011-12-07_2011-12-18/5/Sage-75643/D0ENMACXX.5.recal_data.csv preserve_qscores_less_than=5 smoothing=1 max_quality_score=50 doNotWriteOriginalQuals=false no_pg_tag=false fail_with_no_eof_marker=false skipUQUpdate=false Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate]
@PG	ID:GATK TableRecalibration.4	VN:1.3-14-g59da26a	CL:default_read_group=null default_platform=null force_read_group=null force_platform=null window_size_nqs=5 homopolymer_nback=7 exception_if_no_tile=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION recal_file=/seq/picard/D0ENMACXX/C1-210_2011-12-07_2011-12-18/6/Sage-75643/D0ENMACXX.6.recal_data.csv preserve_qscores_less_than=5 smoothing=1 max_quality_score=50 doNotWriteOriginalQuals=false no_pg_tag=false fail_with_no_eof_marker=false skipUQUpdate=false Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate]
@PG	ID:GATK TableRecalibration.5	VN:1.3-14-g59da26a	CL:default_read_group=null default_platform=null force_read_group=null force_platform=null window_size_nqs=5 homopolymer_nback=7 exception_if_no_tile=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION recal_file=/seq/picard/D0ENMACXX/C1-210_2011-12-07_2011-12-18/2/Sage-75643/D0ENMACXX.2.recal_data.csv preserve_qscores_less_than=5 smoothing=1 max_quality_score=50 doNotWriteOriginalQuals=false no_pg_tag=false fail_with_no_eof_marker=false skipUQUpdate=false Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate]
@PG	ID:bwa	PN:bwa	VN:0.5.9-r16	CL:bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.1.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.1.Sage-75643.2.fastq.gz; bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.1.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.1.Sage-75643.1.fastq.gz; bwa sampe -P -f D0ENMACXX.1.Sage-75643.Homo_sapiens_assembly19.aligned_bwa.sam Homo_sapiens_assembly19.fasta D0ENMACXX.1.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.1.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.1.Sage-75643.1.fastq.gz D0ENMACXX.1.Sage-75643.2.fastq.gz
@PG	ID:bwa.1	PN:bwa	VN:0.5.9-r16	CL:bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.3.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.3.Sage-75643.2.fastq.gz; bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.3.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.3.Sage-75643.1.fastq.gz; bwa sampe -P -f D0ENMACXX.3.Sage-75643.Homo_sapiens_assembly19.aligned_bwa.sam Homo_sapiens_assembly19.fasta D0ENMACXX.3.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.3.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.3.Sage-75643.1.fastq.gz D0ENMACXX.3.Sage-75643.2.fastq.gz
@PG	ID:bwa.2	PN:bwa	VN:0.5.9-r16	CL:bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.7.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.7.Sage-75643.2.fastq.gz; bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.7.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.7.Sage-75643.1.fastq.gz; bwa sampe -P -f D0ENMACXX.7.Sage-75643.Homo_sapiens_assembly19.aligned_bwa.sam Homo_sapiens_assembly19.fasta D0ENMACXX.7.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.7.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.7.Sage-75643.1.fastq.gz D0ENMACXX.7.Sage-75643.2.fastq.gz
@PG	ID:bwa.3	PN:bwa	VN:0.5.9-r16	CL:bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.5.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.5.Sage-75643.2.fastq.gz; bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.5.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.5.Sage-75643.1.fastq.gz; bwa sampe -P -f D0ENMACXX.5.Sage-75643.Homo_sapiens_assembly19.aligned_bwa.sam Homo_sapiens_assembly19.fasta D0ENMACXX.5.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.5.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.5.Sage-75643.1.fastq.gz D0ENMACXX.5.Sage-75643.2.fastq.gz
@PG	ID:bwa.4	PN:bwa	VN:0.5.9-r16	CL:bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.6.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.6.Sage-75643.2.fastq.gz; bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.6.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.6.Sage-75643.1.fastq.gz; bwa sampe -P -f D0ENMACXX.6.Sage-75643.Homo_sapiens_assembly19.aligned_bwa.sam Homo_sapiens_assembly19.fasta D0ENMACXX.6.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.6.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.6.Sage-75643.1.fastq.gz D0ENMACXX.6.Sage-75643.2.fastq.gz
@PG	ID:bwa.5	PN:bwa	VN:0.5.9-r16	CL:bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.2.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.2.Sage-75643.2.fastq.gz; bwa aln Homo_sapiens_assembly19.fasta -q 5 -l 32 -k 2 -t 4 -o 1 -f D0ENMACXX.2.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.2.Sage-75643.1.fastq.gz; bwa sampe -P -f D0ENMACXX.2.Sage-75643.Homo_sapiens_assembly19.aligned_bwa.sam Homo_sapiens_assembly19.fasta D0ENMACXX.2.Sage-75643.Homo_sapiens_assembly19.1.sai D0ENMACXX.2.Sage-75643.Homo_sapiens_assembly19.2.sai D0ENMACXX.2.Sage-75643.1.fastq.gz D0ENMACXX.2.Sage-75643.2.fastq.gz
@PG	ID:GATK IndelRealigner	VN:1.3-14-g59da26a	CL:knownAlleles=[(RodBinding name=knownAlleles source=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.vcf), (RodBinding name=knownAlleles2 source=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf)] LODThresholdForCleaning=5.0 out=null bam_compression=null disable_bam_indexing=null generate_md5=null simplifyBAM=null consensusDeterminationModel=USE_SW entropyThreshold=0.15 maxReadsInMemory=1000000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=/seq/picard_aggregation/G15511/HCC1143/v1/final_bams.map generate_nWayOut_md5s=true check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=/seq/picard_aggregation/G15511/HCC1143/v1/HCC1143.indel.stats SNPsFileForDebugging=null
@CO	aggregation_version=1