Galaxy History ' asp5 leaf example'


DatasetAnnotation
1: asp5_leaf_read1.P001.fq
136.7 Mb
format: fastq, database: Populus_unmasked
Info: uploaded fastq file
@SOLEXA14:5:1:1:1424#0/1
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+SOLEXA14:5:1:1:1424#0/1
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@SOLEXA14:5:1:2:1420#0/1
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2: asp5_leaf_read2.P001.fq
136.7 Mb
format: fastq, database: Populus_unmasked
Info: uploaded fastq file
@SOLEXA14:5:1:1:1424#0/2
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5: FASTQ Groomer on data 1
136.7 Mb
format: fastqsanger, database: Populus_unmasked
Info: Groomed 899422 illumina reads into sanger reads.
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6: FASTQ Groomer on data 2
136.7 Mb
format: fastqsanger, database: Populus_unmasked
Info: Groomed 899422 illumina reads into sanger reads.
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7: Map with BWA for Illumina on data 6 and data 5: mapped reads
~2,700,000 lines, 2,520 comments
format: sam, database: Populus_unmasked
Info: BWA Version: 0.5.9-r16
BWA run on paired-end data
1.QNAME2.FLAG3.RNAME4.POS5.MAPQ6.CIGAR7.MRNM8.MPOS9.ISIZE10.SEQ11.QUAL12.OPT
@SQ SN:scaffold_1 LN:48367220
@SQ SN:scaffold_2 LN:23562801
@SQ SN:scaffold_3 LN:20216605
@SQ SN:scaffold_4 LN:23188140
@SQ SN:scaffold_5 LN:25802683
@SQ SN:scaffold_6 LN:26894541
8: SAM-to-BAM on data 7: converted BAM
96.2 Mb
format: bam, database: Populus_unmasked
Info: Samtools Version: 0.1.18 (r982:295)
SAM file converted to BAM
Binary bam alignments file
9: flagstat on data 8
11 lines
format: txt, database: Populus_unmasked
1798844 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
1391834 + 0 mapped (77.37%:-nan%)
1798844 + 0 paired in sequencing
899422 + 0 read1
899422 + 0 read2
50: Realigner Target Creator on data 8 (GATK intervals)
28,429 lines
format: gatk_interval, database: Populus_unmasked
scaffold_1:112937-112939
scaffold_1:116902-116903
scaffold_1:131668-131676
scaffold_1:132272-132273
scaffold_1:139146-139151
scaffold_1:139629
51: Realigner Target Creator on data 8 (log)
27 lines
format: txt, database: Populus_unmasked
INFO 14:35:57,176 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:35:57,178 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:35:57,178 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:35:57,178 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:35:57,178 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:35:57,179 HelpFormatter - Program Args: -T RealignerTargetCreator -o /mnt/spruce/storage/ftp/database/files/003/dataset_3780.dat -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa -I /tmp/tmpkqyFlV/gatk_input.bam
52: Indel Realigner on data 50 and data 8 (BAM)
98.7 Mb
format: bam, database: Populus_unmasked
Binary bam alignments file
53: Indel Realigner on data 50 and data 8 (log)
18 lines
format: txt, database: Populus_unmasked
INFO 14:45:45,650 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:45:45,652 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:45:45,652 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:45:45,653 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:45:45,653 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:45:45,653 HelpFormatter - Program Args: -T IndelRealigner -o /mnt/spruce/storage/ftp/database/files/003/dataset_3782.dat -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa -LOD 5.0 --disable_bam_indexing -I /tmp/tmpIbHUEj/gatk_input.ba
54: Count Covariates on data 52 (Covariate File)
40 lines, 4 comments
format: csv, database: Populus_unmasked
1
# Counted Sites 20677196
# Counted Bases 64260314
# Skipped Sites 0
# Fraction Skipped 1 / Infinity bp
ReadGroup,QualityScore,nObservations,nMismatches,Qempirical
Asp5,2,2581891,156861,12
55: Count Covariates on data 52 (log)
32 lines
format: txt, database: Populus_unmasked
INFO 14:46:31,102 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:46:31,104 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:46:31,104 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:46:31,104 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:46:31,104 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:46:31,105 HelpFormatter - Program Args: -T CountCovariates --num_threads 4 -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa --recal_file /mnt/spruce/storage/ftp/database/files/003/dataset_3784.dat -cov ReadGroupCovariate -cov Quality
56: Table Recalibration on data 54 and data 52 (BAM)
108.2 Mb
format: bam, database: Populus_unmasked
Binary bam alignments file
57: Table Recalibration on data 54 and data 52 (log)
25 lines
format: txt, database: Populus_unmasked
INFO 14:47:19,787 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:47:19,789 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:47:19,789 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:47:19,789 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:47:19,789 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:47:19,790 HelpFormatter - Program Args: -T TableRecalibration -o /mnt/spruce/storage/ftp/database/files/003/dataset_3786.dat -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa --recal_file /mnt/spruce/storage/ftp/database/files/003/dat
58: Unified Genotyper on data 56 (VCF)
88,517 lines, 2,544 comments
format: vcf, database: Populus_unmasked
1.Chrom2.Pos3.ID4.Ref5.Alt6.Qual7.Filter8.Info9.Format10.data
##fileformat=VCFv4.1
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
59: Unified Genotyper on data 56 (log)
42 lines
format: txt, database: Populus_unmasked
INFO 14:48:07,428 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:48:07,430 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:48:07,430 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:48:07,431 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:48:07,431 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:48:07,431 HelpFormatter - Program Args: -T UnifiedGenotyper -o /mnt/spruce/storage/ftp/database/files/003/dataset_3788.dat -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa --standard_min_confidence_threshold_for_calling 30.0 --standa