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Removed the dependency on samtools from the unit tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| @HD VN:1.4 SO:unsorted | ||
| @PG ID:SCS PN:HiSeq Control Software DS:Controlling software on instrument VN:2.0.12.0 | ||
| @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.17.21.3 | ||
| @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.13 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities BASECALLS_DIR=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=ERS427447,ERS427448,ERS427449,ERS427450,ERS427451,ERS427452,ERS427453,ERS427454,ERS427455,ERS427456,ERS427457,ERS427458,phiX_for_spiked_buffers STUDY_NAME=Illumina Controls: SPIKED_CONTROL,ERP005431: High-throughput RNA sequencing of the main olfactory epithelium of odour-exposed mice. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | ||
| @PG ID:bamadapterfind PN:bamadapterfind PP:Illumina2bam VN:0.0.129 CL:bamadapterfind level=0 | ||
| @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind DS:A command-line tool to decode multiplexed bam file VN:V1.13 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/12693_1.bam BARCODE_FILE=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/lane_1.taglist METRICS_FILE=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/12693_1.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true BARCODE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 CONVERT_LOW_QUALITY_TO_NO_CALL=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | ||
| @PG ID:spf PN:spatial_filter PP:BamIndexDecoder DS:A program to apply a spatial filter VN:v10.14 CL:/software/solexa/pkg/pb_calibration/v10.14/bin/spatial_filter -c -F pb_align_12693_1.bam.filter -t /nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/no_cal/archive/qc/tileviz/12693_1 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_12693_1.bam ; /software/solexa/pkg/pb_calibration/v10.14/bin/spatial_filter -a -u -F pb_align_12693_1.bam.filter - | ||
| @PG ID:bwa PN:bwa PP:spf VN:0.5.10-tpx | ||
| @PG ID:BamMerger PN:BamMerger PP:bwa DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM VN:V1.13 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_12693_1.bam INPUT=/dev/stdin OUTPUT=12693_1.bam KEEP_EXTRA_UNMAPPED_READS=true REPLACE_ALIGNED_BASE_QUALITY=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true ALIGNMENT_PROGRAM_ID=bwa KEEP_ALL_PG=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | ||
| @PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs VN:V1.13 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/no_cal/12693_1.bam OUTPUT_PREFIX=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/no_cal/lane1/12693_1 OUTPUT_COMMON_RG_HEAD_TO_TRIM=1 VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | ||
| @PG ID:bambi PN:bambi PP:SplitBamByReadGroup VN:12.34 CL:bambi select -i /nfs/users/nfs_j/js10/npg/bambi/test/data/read2tags.sam -o /tmp/bambi.W6cJH8/read2tags_1.bam -t Ba -q Qa -p 1:1:1 DS:convert reads to tags | ||
| @PG ID:samtools PN:samtools PP:bambi VN:1.18 CL:/usr/local/bin/samtools view -h -o read2tags_1.sam read2tags_1.bam | ||
| @SQ SN:phix-illumina.fa LN:5386 | ||
| @RG ID:1#0 PL:ILLUMINA PU:140420_HS31_12693_A_H8M2LADXX_1#0 LB:unknown DS:Study Illumina Controls: SPIKED_CONTROL,ERP005431: High-throughput RNA sequencing of the main olfactory epithelium of odour-exposed mice. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2014-04-20T00:00:00+0100 SM:ERS427447,ERS427448,ERS427449,ERS427450,ERS427451,ERS427452,ERS427453,ERS427454,ERS427455,ERS427456,ERS427457,ERS427458,phiX_for_spiked_buffers PG:BamIndexDecoder CN:SC | ||
| HS31_12693:1:1101:5133:2240#0 77 * 0 0 * * 0 0 CTGTAAAAATTTGGTATTG HHHHHHFFFFFFEEBEEED BC:Z:TTGGCATC RG:Z:1#0 QT:Z:CCCFFFFE ci:i:215 Ba:Z:A Qa:Z:H | ||
| HS31_12693:1:1101:5133:2240#0 141 * 0 0 * * 0 0 TAGCTGTAGCAAAATTACAG EECDDDDDDDDDDDDDDDDD RG:Z:1#0 ci:i:215 | ||
| HS31_12693:1:1101:10450:2212#0 77 * 0 0 * * 0 0 AGGCGCAGTCTGTCAATGC DDDDDDDDBDDDDDDEEDD BC:Z:TTTTATTT RG:Z:1#0 QT:Z:-71(())) ci:i:472 Ba:Z:C Qa:Z:D | ||
| HS31_12693:1:1101:11147:2231#0 141 * 0 0 * * 0 0 GGACTAGGAATGCCAGTAAG EECDDDDDCDDDDDDCCDC@ RG:Z:1#0 ci:i:513 | ||
| HS31_12693:1:1101:11999:2206#0 77 * 0 0 * * 0 0 CGCTGAGAATCCCATTGAC FFDDDDDDDDDDDDDDDDD BC:Z:AAGTGATC RG:Z:1#0 QT:Z:BCCDFFFD ci:i:538 Ba:Z:C Qa:Z:F | ||
| HS31_12693:1:1101:11999:2206#0 141 * 0 0 * * 0 0 TTCAAAGCTTTTTAGACAAC ECEEEDDDDDDDDDDDDDDD RG:Z:1#0 ci:i:538 | ||
| HS31_12693:1:1101:12330:2229#0 77 * 0 0 * * 0 0 AGAAGCCAGAGTCCTTGTC DDDDDDDDDDDACDDDDDD BC:Z:TCACGATC RG:Z:1#0 QT:Z:CCCFFFDD ci:i:573 Ba:Z:G Qa:Z:D | ||
| HS31_12693:1:1101:12330:2229#0 141 * 0 0 * * 0 0 CAGATGGAGTCAGAGGACAT DDDDDDDDDDDDDDDDDDDD RG:Z:1#0 ci:i:573 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| @HD VN:1.4 SO:unsorted | ||
| @PG ID:SCS PN:HiSeq Control Software DS:Controlling software on instrument VN:2.0.12.0 | ||
| @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.17.21.3 | ||
| @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.13 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities BASECALLS_DIR=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=ERS427447,ERS427448,ERS427449,ERS427450,ERS427451,ERS427452,ERS427453,ERS427454,ERS427455,ERS427456,ERS427457,ERS427458,phiX_for_spiked_buffers STUDY_NAME=Illumina Controls: SPIKED_CONTROL,ERP005431: High-throughput RNA sequencing of the main olfactory epithelium of odour-exposed mice. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | ||
| @PG ID:bamadapterfind PN:bamadapterfind PP:Illumina2bam VN:0.0.129 CL:bamadapterfind level=0 | ||
| @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind DS:A command-line tool to decode multiplexed bam file VN:V1.13 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/12693_1.bam BARCODE_FILE=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/lane_1.taglist METRICS_FILE=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/12693_1.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true BARCODE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 CONVERT_LOW_QUALITY_TO_NO_CALL=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | ||
| @PG ID:spf PN:spatial_filter PP:BamIndexDecoder DS:A program to apply a spatial filter VN:v10.14 CL:/software/solexa/pkg/pb_calibration/v10.14/bin/spatial_filter -c -F pb_align_12693_1.bam.filter -t /nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/no_cal/archive/qc/tileviz/12693_1 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_12693_1.bam ; /software/solexa/pkg/pb_calibration/v10.14/bin/spatial_filter -a -u -F pb_align_12693_1.bam.filter - | ||
| @PG ID:bwa PN:bwa PP:spf VN:0.5.10-tpx | ||
| @PG ID:BamMerger PN:BamMerger PP:bwa DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM VN:V1.13 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_12693_1.bam INPUT=/dev/stdin OUTPUT=12693_1.bam KEEP_EXTRA_UNMAPPED_READS=true REPLACE_ALIGNED_BASE_QUALITY=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true ALIGNMENT_PROGRAM_ID=bwa KEEP_ALL_PG=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | ||
| @PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs VN:V1.13 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/no_cal/12693_1.bam OUTPUT_PREFIX=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/no_cal/lane1/12693_1 OUTPUT_COMMON_RG_HEAD_TO_TRIM=1 VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | ||
| @PG ID:bambi PN:bambi PP:SplitBamByReadGroup VN:12.34 CL:bambi select -i /nfs/users/nfs_j/js10/npg/bambi/test/data/read2tags.sam -o /tmp/bambi.DqGa7o/read2tags_10.bam -t BC -q QT -p 2:1:999 -d ci,RG -k BC,QT --replace DS:convert reads to tags | ||
| @PG ID:samtools PN:samtools PP:bambi VN:1.18 CL:/usr/local/bin/samtools view -h -o read2tags_10.sam read2tags_10.bam | ||
| @SQ SN:phix-illumina.fa LN:5386 | ||
| @RG ID:1#0 PL:ILLUMINA PU:140420_HS31_12693_A_H8M2LADXX_1#0 LB:unknown DS:Study Illumina Controls: SPIKED_CONTROL,ERP005431: High-throughput RNA sequencing of the main olfactory epithelium of odour-exposed mice. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2014-04-20T00:00:00+0100 SM:ERS427447,ERS427448,ERS427449,ERS427450,ERS427451,ERS427452,ERS427453,ERS427454,ERS427455,ERS427456,ERS427457,ERS427458,phiX_for_spiked_buffers PG:BamIndexDecoder CN:SC | ||
| HS31_12693:1:1101:5133:2240#0 4 * 0 0 * * 0 0 ACTGTAAAAATTTGGTATTG HHHHHHHFFFFFFEEBEEED RG:Z:1#0 ci:i:215 BC:Z:TAGCTGTAGCAAAATTACAG QT:Z:EECDDDDDDDDDDDDDDDDD | ||
| HS31_12693:1:1101:10450:2212#0 77 * 0 0 * * 0 0 CAGGCGCAGTCTGTCAATGC DDDDDDDDDBDDDDDDEEDD BC:Z:TTTTATTT RG:Z:1#0 QT:Z:-71(())) ci:i:472 | ||
| HS31_12693:1:1101:11147:2231#0 141 * 0 0 * * 0 0 * * RG:Z:1#0 ci:i:513 BC:Z:GGACTAGGAATGCCAGTAAG QT:Z:EECDDDDDCDDDDDDCCDC@ | ||
| HS31_12693:1:1101:11999:2206#0 4 * 0 0 * * 0 0 CCGCTGAGAATCCCATTGAC FFFDDDDDDDDDDDDDDDDD RG:Z:1#0 ci:i:538 BC:Z:TTCAAAGCTTTTTAGACAAC QT:Z:ECEEEDDDDDDDDDDDDDDD | ||
| HS31_12693:1:1101:12330:2229#0 4 * 0 0 * * 0 0 GAGAAGCCAGAGTCCTTGTC DDDDDDDDDDDDACDDDDDD RG:Z:1#0 ci:i:573 BC:Z:CAGATGGAGTCAGAGGACAT QT:Z:DDDDDDDDDDDDDDDDDDDD |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| @HD VN:1.4 SO:unsorted | ||
| @PG ID:SCS PN:HiSeq Control Software DS:Controlling software on instrument VN:2.0.12.0 | ||
| @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.17.21.3 | ||
| @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.13 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities BASECALLS_DIR=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=ERS427447,ERS427448,ERS427449,ERS427450,ERS427451,ERS427452,ERS427453,ERS427454,ERS427455,ERS427456,ERS427457,ERS427458,phiX_for_spiked_buffers STUDY_NAME=Illumina Controls: SPIKED_CONTROL,ERP005431: High-throughput RNA sequencing of the main olfactory epithelium of odour-exposed mice. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | ||
| @PG ID:bamadapterfind PN:bamadapterfind PP:Illumina2bam VN:0.0.129 CL:bamadapterfind level=0 | ||
| @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind DS:A command-line tool to decode multiplexed bam file VN:V1.13 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/12693_1.bam BARCODE_FILE=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/lane_1.taglist METRICS_FILE=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/12693_1.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true BARCODE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 CONVERT_LOW_QUALITY_TO_NO_CALL=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | ||
| @PG ID:spf PN:spatial_filter PP:BamIndexDecoder DS:A program to apply a spatial filter VN:v10.14 CL:/software/solexa/pkg/pb_calibration/v10.14/bin/spatial_filter -c -F pb_align_12693_1.bam.filter -t /nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/no_cal/archive/qc/tileviz/12693_1 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_12693_1.bam ; /software/solexa/pkg/pb_calibration/v10.14/bin/spatial_filter -a -u -F pb_align_12693_1.bam.filter - | ||
| @PG ID:bwa PN:bwa PP:spf VN:0.5.10-tpx | ||
| @PG ID:BamMerger PN:BamMerger PP:bwa DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM VN:V1.13 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_12693_1.bam INPUT=/dev/stdin OUTPUT=12693_1.bam KEEP_EXTRA_UNMAPPED_READS=true REPLACE_ALIGNED_BASE_QUALITY=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true ALIGNMENT_PROGRAM_ID=bwa KEEP_ALL_PG=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | ||
| @PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs VN:V1.13 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/no_cal/12693_1.bam OUTPUT_PREFIX=/nfs/sf32/ILorHSany_sf32/analysis/140420_HS31_12693_A_H8M2LADXX/Data/Intensities/BAM_basecalls_20140421-132642/no_cal/lane1/12693_1 OUTPUT_COMMON_RG_HEAD_TO_TRIM=1 VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | ||
| @PG ID:bambi PN:bambi PP:SplitBamByReadGroup VN:12.34 CL:bambi select -i /nfs/users/nfs_j/js10/npg/bambi/test/data/read2tags.sam -o /tmp/bambi.W6cJH8/read2tags_1.bam -t Ba -q Qa -p 1:1:1 DS:convert reads to tags | ||
| @PG ID:samtools PN:samtools PP:bambi VN:1.18 CL:/usr/local/bin/samtools view -h read2tags_1.bam | ||
| @PG ID:samtools.1 PN:samtools PP:samtools VN:1.18 CL:/usr/local/bin/samtools view -O bam -o read2tags_11.bam read2tags_11.sam | ||
| @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.18 CL:/usr/local/bin/samtools view -h -o read2tags_11.sam read2tags_11.bam | ||
| @SQ SN:phix-illumina.fa LN:5386 | ||
| @RG ID:1#0 PL:ILLUMINA PU:140420_HS31_12693_A_H8M2LADXX_1#0 LB:unknown DS:Study Illumina Controls: SPIKED_CONTROL,ERP005431: High-throughput RNA sequencing of the main olfactory epithelium of odour-exposed mice. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2014-04-20T00:00:00+0100 SM:ERS427447,ERS427448,ERS427449,ERS427450,ERS427451,ERS427452,ERS427453,ERS427454,ERS427455,ERS427456,ERS427457,ERS427458,phiX_for_spiked_buffers PG:BamIndexDecoder CN:SC | ||
| HS31_12693:1:1101:5133:2240#0 77 * 0 0 * * 0 0 CTGTAAAAATTTGGTATTG HHHHHHFFFFFFEEBEEED BC:Z:TTGGCATC RG:Z:1#0 QT:Z:CCCFFFFE ci:i:215 | ||
| HS31_12693:1:1101:5133:2240#0 141 * 0 0 * * 0 0 TAGCTGTAGCAAAATTACAG EECDDDDDDDDDDDDDDDDD RG:Z:1#0 ci:i:215 Ba:Z:A Qa:Z:H | ||
| HS31_12693:1:1101:10450:2212#0 77 * 0 0 * * 0 0 AGGCGCAGTCTGTCAATGC DDDDDDDDBDDDDDDEEDD BC:Z:TTTTATTT RG:Z:1#0 QT:Z:-71(())) ci:i:472 | ||
| HS31_12693:1:1101:11147:2231#0 141 * 0 0 * * 0 0 GGACTAGGAATGCCAGTAAG EECDDDDDCDDDDDDCCDC@ RG:Z:1#0 ci:i:513 | ||
| HS31_12693:1:1101:11999:2206#0 77 * 0 0 * * 0 0 CGCTGAGAATCCCATTGAC FFDDDDDDDDDDDDDDDDD BC:Z:AAGTGATC RG:Z:1#0 QT:Z:BCCDFFFD ci:i:538 | ||
| HS31_12693:1:1101:11999:2206#0 141 * 0 0 * * 0 0 TTCAAAGCTTTTTAGACAAC ECEEEDDDDDDDDDDDDDDD RG:Z:1#0 ci:i:538 Ba:Z:C Qa:Z:F | ||
| HS31_12693:1:1101:12330:2229#0 77 * 0 0 * * 0 0 AGAAGCCAGAGTCCTTGTC DDDDDDDDDDDACDDDDDD BC:Z:TCACGATC RG:Z:1#0 QT:Z:CCCFFFDD ci:i:573 | ||
| HS31_12693:1:1101:12330:2229#0 141 * 0 0 * * 0 0 CAGATGGAGTCAGAGGACAT DDDDDDDDDDDDDDDDDDDD RG:Z:1#0 ci:i:573 Ba:Z:G Qa:Z:D |
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