@HD VN:1.5 GO:none SO:coordinate @PG ID:AlignmentFilter PN:AlignmentFilter PP:bamsormadup VN:V1.19 DS:Give a list of SAM/BAM files with the same set of records and in the same order but aligned with different references, split reads into different files according to alignments. You have option to put unaligned reads into one of output files or a separate file CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[./initial_phix_aln_19663_7#24.bam, /tmp/uKbpdwEgcj/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/zXFhRHgcYS/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=19663_7#24.bam_alignment_filter_metrics.json VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind VN:V1.19 DS:A command-line tool to decode multiplexed bam file CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities/BAM_basecalls_20160512-101540/metadata_cache_19663/lane_7.taglist METRICS_FILE=/nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities/BAM_basecalls_20160512-101540/19663_7.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=false 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 CHANGE_READ_NAME=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:BamMerger PN:BamMerger PP:bwa VN:V1.19 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 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_19663_7.bam INPUT=/dev/stdin OUTPUT=19663_7.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:GATK IndelRealigner VN:3.5-0-ge91472d CL:knownAlleles=[] targetIntervals=/lustre/scratch115/projects/ddd/vrpipe-ihtp_fy5/output/8/0/0/1272b4365f72e7485fdcda21ef917/912987/4_gatk_target_interval_creator_discovery/pe.1.bam.intervals LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling VN:V1.19 DS:Convert Illumina BCL to BAM or SAM file CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities BASECALLS_DIR=/nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities/BaseCalls LANE=7 OUTPUT=/dev/stdout READ_GROUP_ID=19663_7 SAMPLE_ALIAS=DDD_MAIN6251881,DDD_MAIN6251882,DDD_MAIN6251884,DDD_MAIN6251888,DDD_MAIN6251890,DDD_MAIN6251891,DDD_MAIN6251892,DDD_MAIN6251893,DDD_MAIN6251894,DDD_MAIN6251895,DDD_MAIN6251896,DDD_MAIN6251899,DDD_MAIN6251900,DDD_MAIN6251903,DDD_MAIN6251904,DDD_MAIN6251905,DDD_MAIN6251906,DDD_MAIN6251907,DDD_MAIN6251909,DDD_MAIN6251910,DDD_MAIN6251911,DDD_MAIN6251912,DDD_MAIN6251913,DDD_MAIN6252143 STUDY_NAME=EGAS00001001609: We propose to apply state of the art molecular testing, including SNP genotyping, to 12,000 UK children with abnormal development. The results will provide a unique, on-line catalogue of genetic changes linked to symptoms that will enable clinicians to diagnose developmental disorders. Furthermore, we will design more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with abnormal development. PLATFORM_UNIT=160508_HS31_19663_A_C94TDANXX_7 COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT ADD_CLUSTER_INDEX_TAG=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:MarkDuplicates PN:MarkDuplicates VN:1.114(444810c1de1433d9eca8130be63ccc7fd70a9499_1400593393) CL:picard.sam.MarkDuplicates INPUT=[/lustre/scratch115/projects/ddd/vrpipe-ihtp_fy5/output/7/7/e/b8aadf158d7cdd8643ecd2e1f33e9/902397/2_bam_merge/pe.1.bam] OUTPUT=/lustre/scratch115/projects/ddd/vrpipe-ihtp_fy5/output/7/7/e/b8aadf158d7cdd8643ecd2e1f33e9/902397/3_bam_mark_duplicates/pe.1.markdup.bam METRICS_FILE=/dev/null ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates REMOVE_DUPLICATES=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:SCS PN:HiSeq Control Software VN:2.2.68 DS:Controlling software on instrument @PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger VN:V1.19 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 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities/BAM_basecalls_20160512-101540/no_cal/19663_7.bam OUTPUT_PREFIX=/nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities/BAM_basecalls_20160512-101540/no_cal/lane7/ VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:bam12split PN:bam12split PP:samtools VN:2.0.37 CL:/software/solexa/pkg/biobambam/2.0.37/bin/bam12split verbose=0 level=0 @PG ID:bamadapterclip PN:bamadapterclip PP:bamreset VN:2.0.37 CL:/software/solexa/pkg/biobambam/2.0.37/bin/bamadapterclip verbose=0 level=0 @PG ID:bamadapterfind PN:bamadapterfind PP:Illumina2bam VN:2.0.37 CL:bamadapterfind level=0 @PG ID:bamcollate2 PN:bamcollate2 PP:SplitBamByReadGroup VN:2.0.37 CL:/software/solexa/pkg/biobambam/2.0.37/bin/bamcollate2 collate=1 level=0 @PG ID:bamreset PN:bamreset PP:bamcollate2 VN:2.0.37 CL:/software/solexa/pkg/biobambam/2.0.37/bin/bamreset resetaux=0 level=0 verbose=0 @PG ID:bamsormadup PN:bamsormadup PP:bam12split VN:2.0.37 CL:/software/solexa/pkg/biobambam/2.0.37/bin/bamsormadup threads=16 SO=queryname level=0 @PG ID:bamsort PN:bamsort PP:AlignmentFilter VN:2.0.37 CL:/software/solexa/pkg/biobambam/2.0.37/bin/bamsort SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities/BAM_basecalls_20160512-101540/no_cal/archive/lane7/bsfopt_19663_7#24.tmp @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates PP:bamsort VN:2.0.37 CL:/software/solexa/pkg/biobambam/2.0.37/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities/BAM_basecalls_20160512-101540/no_cal/archive/lane7/bmdfopt_19663_7#24.tmp M=/nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities/BAM_basecalls_20160512-101540/no_cal/archive/lane7/19663_7#24.markdups_metrics.txt @PG ID:basecalling PN:RTA PP:SCS VN:1.18.66.3 DS:Basecalling Package @PG ID:bwa PN:bwa PP:spf VN:0.5.10-tpx @PG ID:bwa' PN:bwa PP:bamadapterclip VN:0.7.13-r1126 CL:/software/solexa/pkg/bwa/0.7.13/bwa mem -t 16 -p -T 0 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/T9VpWpqf8G/alntgt_bamtofastq_out @PG ID:samtools PN:samtools PP:scramble VN:1.3-npg-Apr2016 CL:/software/solexa/pkg/samtools/1.3-npg-Apr2016/bin/samtools reheader /tmp/HiAoJeBUCq/postalntgt_alterSQ_headerSQfix_out /tmp/Oy1Kt3GXjM/postalntgt_mbuffer_headerSQfix_out @PG ID:scramble PN:scramble PP:bwa' VN:1.14.7 CL:/software/solexa/pkg/scramble/1.14.7/bin/scramble -0 -I sam -O bam @PG ID:scramble.1 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.7 CL:/software/solexa/pkg/scramble/1.14.7/bin/scramble -t 7 -7 -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @PG ID:spf PN:spatial_filter PP:BamIndexDecoder VN:v10.26-dirty DS:A program to apply a spatial filter CL:/software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -c -F pb_align_19663_7.bam.filter -t /nfs/sf44/ILorHSany_sf44/analysis/160508_HS31_19663_A_C94TDANXX/Data/Intensities/BAM_basecalls_20160512-101540/no_cal/archive/qc/tileviz/19663_7 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_19663_7.bam ; /software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -a -f -u -F pb_align_19663_7.bam.filter - @PG ID:GATK PrintReads VN:3.5-0-ge91472d CL:readGroup=null platform=null number=-1 sample_file=[] sample_name=[] simplify=false no_pg_tag=false @SQ SN:1 LN:249250621 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Human @SQ SN:2 LN:243199373 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:a0d9851da00400dec1098a9255ac712e SP:Human @SQ SN:3 LN:198022430 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:fdfd811849cc2fadebc929bb925902e5 SP:Human @SQ SN:4 LN:191154276 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:23dccd106897542ad87d2765d28a19a1 SP:Human @SQ SN:5 LN:180915260 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:0740173db9ffd264d728f32784845cd7 SP:Human @SQ SN:6 LN:171115067 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:1d3a93a248d92a729ee764823acbbc6b SP:Human @SQ SN:7 LN:159138663 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:618366e953d6aaad97dbe4777c29375e SP:Human @SQ SN:8 LN:146364022 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:96f514a9929e410c6651697bded59aec SP:Human @SQ SN:9 LN:141213431 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:3e273117f15e0a400f01055d9f393768 SP:Human @SQ SN:10 LN:135534747 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:988c28e000e84c26d552359af1ea2e1d SP:Human @SQ SN:11 LN:135006516 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Human @SQ SN:12 LN:133851895 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:51851ac0e1a115847ad36449b0015864 SP:Human @SQ SN:13 LN:115169878 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:283f8d7892baa81b510a015719ca7b0b SP:Human @SQ SN:14 LN:107349540 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:98f3cae32b2a2e9524bc19813927542e SP:Human @SQ SN:15 LN:102531392 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:e5645a794a8238215b2cd77acb95a078 SP:Human @SQ SN:16 LN:90354753 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Human @SQ SN:17 LN:81195210 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Human @SQ SN:18 LN:78077248 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Human @SQ SN:19 LN:59128983 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:1aacd71f30db8e561810913e0b72636d SP:Human @SQ SN:20 LN:63025520 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Human @SQ SN:21 LN:48129895 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:2979a6085bfe28e3ad6f552f361ed74d SP:Human @SQ SN:22 LN:51304566 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:a718acaa6135fdca8357d5bfe94211dd SP:Human @SQ SN:X LN:155270560 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:7e0e2e580297b7764e31dbc80c2540dd SP:Human @SQ SN:Y LN:59373566 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Human @SQ SN:MT LN:16569 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:c68f52674c9fb33aef52dcf399755519 SP:Human @SQ SN:GL000207.1 LN:4262 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Human @SQ SN:GL000226.1 LN:15008 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Human @SQ SN:GL000229.1 LN:19913 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Human @SQ SN:GL000231.1 LN:27386 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Human @SQ SN:GL000210.1 LN:27682 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:851106a74238044126131ce2a8e5847c SP:Human @SQ SN:GL000239.1 LN:33824 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:99795f15702caec4fa1c4e15f8a29c07 SP:Human @SQ SN:GL000235.1 LN:34474 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Human @SQ SN:GL000201.1 LN:36148 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Human @SQ SN:GL000247.1 LN:36422 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:7de00226bb7df1c57276ca6baabafd15 SP:Human @SQ SN:GL000245.1 LN:36651 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:89bc61960f37d94abf0df2d481ada0ec SP:Human @SQ SN:GL000197.1 LN:37175 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Human @SQ SN:GL000203.1 LN:37498 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:96358c325fe0e70bee73436e8bb14dbd SP:Human @SQ SN:GL000246.1 LN:38154 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Human @SQ SN:GL000249.1 LN:38502 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:1d78abec37c15fe29a275eb08d5af236 SP:Human @SQ SN:GL000196.1 LN:38914 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Human @SQ SN:GL000248.1 LN:39786 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:5a8e43bec9be36c7b49c84d585107776 SP:Human @SQ SN:GL000244.1 LN:39929 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:0996b4475f353ca98bacb756ac479140 SP:Human @SQ SN:GL000238.1 LN:39939 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:131b1efc3270cc838686b54e7c34b17b SP:Human @SQ SN:GL000202.1 LN:40103 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:06cbf126247d89664a4faebad130fe9c SP:Human @SQ SN:GL000234.1 LN:40531 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:93f998536b61a56fd0ff47322a911d4b SP:Human @SQ SN:GL000232.1 LN:40652 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:3e06b6741061ad93a8587531307057d8 SP:Human @SQ SN:GL000206.1 LN:41001 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Human @SQ SN:GL000240.1 LN:41933 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Human @SQ SN:GL000236.1 LN:41934 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Human @SQ SN:GL000241.1 LN:42152 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Human @SQ SN:GL000243.1 LN:43341 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:cc34279a7e353136741c9fce79bc4396 SP:Human @SQ SN:GL000242.1 LN:43523 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Human @SQ SN:GL000230.1 LN:43691 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:b4eb71ee878d3706246b7c1dbef69299 SP:Human @SQ SN:GL000237.1 LN:45867 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Human @SQ SN:GL000233.1 LN:45941 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:7fed60298a8d62ff808b74b6ce820001 SP:Human @SQ SN:GL000204.1 LN:81310 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:efc49c871536fa8d79cb0a06fa739722 SP:Human @SQ SN:GL000198.1 LN:90085 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:868e7784040da90d900d2d1b667a1383 SP:Human @SQ SN:GL000208.1 LN:92689 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Human @SQ SN:GL000191.1 LN:106433 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Human @SQ SN:GL000227.1 LN:128374 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:a4aead23f8053f2655e468bcc6ecdceb SP:Human @SQ SN:GL000228.1 LN:129120 AS:NCBI37 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SP:Human @SQ SN:GL000211.1 LN:166566 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:7daaa45c66b288847b9b32b964e623d3 SP:Human @SQ SN:GL000199.1 LN:169874 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:569af3b73522fab4b40995ae4944e78e SP:Human @SQ SN:GL000217.1 LN:172149 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:6d243e18dea1945fb7f2517615b8f52e SP:Human @SQ SN:GL000216.1 LN:172294 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:642a232d91c486ac339263820aef7fe0 SP:Human @SQ SN:GL000215.1 LN:172545 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:5eb3b418480ae67a997957c909375a73 SP:Human @SQ SN:GL000205.1 LN:174588 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:d22441398d99caf673e9afb9a1908ec5 SP:Human @SQ SN:GL000219.1 LN:179198 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Human @SQ SN:GL000224.1 LN:179693 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Human @SQ SN:GL000223.1 LN:180455 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:399dfa03bf32022ab52a846f7ca35b30 SP:Human @SQ SN:GL000195.1 LN:182896 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:5d9ec007868d517e73543b005ba48535 SP:Human @SQ SN:GL000212.1 LN:186858 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:563531689f3dbd691331fd6c5730a88b SP:Human @SQ SN:GL000222.1 LN:186861 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:6fe9abac455169f50470f5a6b01d0f59 SP:Human @SQ SN:GL000200.1 LN:187035 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Human @SQ SN:GL000193.1 LN:189789 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:dbb6e8ece0b5de29da56601613007c2a SP:Human @SQ SN:GL000194.1 LN:191469 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:6ac8f815bf8e845bb3031b73f812c012 SP:Human @SQ SN:GL000225.1 LN:211173 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:63945c3e6962f28ffd469719a747e73c SP:Human @SQ SN:GL000192.1 LN:547496 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:325ba9e808f669dfeee210fdd7b470ac SP:Human @SQ SN:NC_007605 LN:171823 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:6743bd63b3ff2b5b8985d8933c53290a SP:Human @SQ SN:hs37d5 LN:35477943 AS:NCBI37 UR:/lustre/scratch115/resources/vrpipe/ref/Homo_sapiens/hs37d5.fa M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1 SP:Human @RG ID:19663_7#24 PL:ILLUMINA PU:160508_HS31_19663_A_C94TDANXX_7#24 LB:16357620 DS:EGAS00001001609: We propose to apply state of the art molecular testing, including SNP genotyping, to 12,000 UK children with abnormal development. The results will provide a unique, on-line catalogue of genetic changes linked to symptoms that will enable clinicians to diagnose developmental disorders. Furthermore, we will design more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with abnormal development. DT:2016-05-08T00:00:00+0100 PG:BamIndexDecoder SM:DDD_MAIN6252143 CN:SC