@HD	VN:1.4	SO:coordinate
@RG	ID:1#68	PL:ILLUMINA	PU:130906_HS32_10723_B_H722PADXX_2#68	LB:8099649	DS:EGAS00001000466: FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.	DT:2013-09-06T00:00:00+0100	SM:EGAN00001171932	CN:SC
@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:V1.10	CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities BASECALLS_DIR=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BaseCalls LANE=2 OUTPUT=/dev/stdout SAMPLE_ALIAS=EGAN00001171865,EGAN00001171866,EGAN00001171867,EGAN00001171868,EGAN00001171869,EGAN00001171870,EGAN00001171871,EGAN00001171872,EGAN00001171873,EGAN00001171874,EGAN00001171875,EGAN00001171876,EGAN00001171877,EGAN00001171878,EGAN00001171879,EGAN00001171880,EGAN00001171881,EGAN00001171882,EGAN00001171883,EGAN00001171884,EGAN00001171885,EGAN00001171886,EGAN00001171887,EGAN00001171888,EGAN00001171889,EGAN00001171890,EGAN00001171891,EGAN00001171892,EGAN00001171893,EGAN00001171894,EGAN00001171895,EGAN00001171896,EGAN00001171897,EGAN00001171898,EGAN00001171899,EGAN00001171900,EGAN00001171901,EGAN00001171902,EGAN00001171903,EGAN00001171904,EGAN00001171905,EGAN00001171906,EGAN00001171907,EGAN00001171908,EGAN00001171909,EGAN00001171910,EGAN00001171911,EGAN00001171912,EGAN00001171913,EGAN00001171914,EGAN00001171915,EGAN00001171916,EGAN00001171917,EGAN00001171918,EGAN00001171919,EGAN00001171920,EGAN00001171921,EGAN00001171922,EGAN00001171923,EGAN00001171924,EGAN00001171925,EGAN00001171926,EGAN00001171927,EGAN00001171928,EGAN00001171929,EGAN00001171930,EGAN00001171931,EGAN00001171932,EGAN00001171933,EGAN00001171934,EGAN00001171935,EGAN00001171936,phiX_for_spiked_buffers LIBRARY_NAME=8099655 STUDY_NAME=EGAS00001000466: FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.,Illumina Controls: SPIKED_CONTROL COMPRESSION_LEVEL=0 CREATE_MD5_FILE=true    GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 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
@PG	ID:BamAdapterFinder	PN:BamAdapterFinder	PP:Illumina2bam	DS:Find short inserts by finding overlapping forward/reverse reads. Note position with a tag.	VN:V1.10	CL:uk.ac.sanger.npg.picard.BamAdapterFinder INPUT=/dev/stdin OUTPUT=/dev/stdout ADAPTER_LENGTH_TAG=a3 ADAPTER_MATCH_TAG=ah VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 CREATE_MD5_FILE=true    MIN_OVERLAP=32 PCT_MISMATCHES=10.0 ADAPTER_MATCH=12 VERBOSITY=INFO QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
@PG	ID:BamIndexDecoder	PN:BamIndexDecoder	PP:BamAdapterFinder	DS:A command-line tool to decode multiplexed bam file	VN:V1.10	CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/10723_2.bam BARCODE_FILE=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/lane_2.taglist METRICS_FILE=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/10723_2.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:pb_cal	PN:predictor_pu	PP:BamIndexDecoder	DS:A program to apply a calibration table	VN:v10.12	CL:/software/solexa/bin/pb_calibration/v10.12/predictor_pu -ct 10723_2_purity_cycle_caltable.txt -intensity-dir /nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities -cstart1 1 -cstart2 84 -u ../10723_2.bam
@PG	ID:spf	PN:spatial_filter	PP:pb_cal	DS:A program to apply a spatial filter	VN:v10.12	CL:/software/solexa/bin/pb_calibration/v10.12/spatial_filter -c  -F pb_align_10723_2.bam.filter --region_size 700 --region_min_count 122 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_10723_2.bam ; /software/solexa/bin/pb_calibration/v10.12/spatial_filter -a  -u  -F pb_align_10723_2.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:V1.10	CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_10723_2.bam INPUT=/dev/stdin OUTPUT=10723_2.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:V1.10	CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/10723_2.bam OUTPUT_PREFIX=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/lane2/10723_2 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:bwa_aln	PN:bwa	PP:SplitBamByReadGroup	VN:0.5.10-tpx	CL:/software/solexa/bin/aligners/bwa/bwa-0.5.10-mt/bwa aln  -t 8 /lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/bwa/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa -b1 /nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/lane2/10723_2#68.bam > /tmp/avbZEHW4Rj/1.sai
@PG	ID:bwa_aln_1	PN:bwa	PP:bwa_aln	VN:0.5.10-tpx	CL:/software/solexa/bin/aligners/bwa/bwa-0.5.10-mt/bwa aln  -t 8 /lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/bwa/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa -b2 /nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/lane2/10723_2#68.bam > /tmp/avbZEHW4Rj/2.sai
@PG	ID:bwa_sam	PN:bwa	PP:bwa_aln_1	VN:0.5.10-tpx	CL:/software/solexa/bin/aligners/bwa/bwa-0.5.10-mt/bwa sampe -t 6 /lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/bwa/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa /tmp/avbZEHW4Rj/1.sai /tmp/avbZEHW4Rj/2.sai /nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/lane2/10723_2#68.bam /nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/lane2/10723_2#68.bam
@PG	ID:Picard_SamFormatConverter	PN:SamFormatConverter	PP:bwa_sam	VN:1.72(1230)	CL:/software/java/bin/java -Xmx1000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/SamFormatConverter.jar VALIDATION_STRINGENCY=SILENT INPUT=/dev/stdin OUTPUT=/dev/stdout COMPRESSION_LEVEL=0
@PG	ID:samtools_fixmate	PN:samtools	PP:Picard_SamFormatConverter	VN:0.1.18 (r982:295)	CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools fixmate - -
@PG	ID:BamMerger_1	PN:BamMerger	PP:samtools_fixmate	VN:V1.10	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=/dev/stdin ALIGNMENT_PROGRAM_ID=NULL KEEP_ALL_PG=true INPUT=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/lane2/10723_2#68.bam OUTPUT=/tmp/avbZEHW4Rj/output_fifo.bam KEEP_EXTRA_UNMAPPED_READS=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true    REPLACE_ALIGNED_BASE_QUALITY=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
@PG	ID:AlignmentFilter	PN:AlignmentFilter	PP:BamMerger_1	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	VN:V1.10	CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/lane2/10723_2#68.bam, /tmp/avbZEHW4Rj/output_fifo.bam] OUTPUT_ALIGNMENT=[/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/archive/lane2/10723_2#68_phix.bam, /nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/archive/lane2/10723_2#68.bam] METRICS_FILE=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/archive/lane2/10723_2#68.bam_alignment_filter_metrics.json VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true    VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
@PG	ID:bamsort	PN:bamsort	PP:AlignmentFilter	VN:0.0.87	CL:/software/hpag/biobambam/0.0.87/bin/bamsort tmpfile=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/archive/lane2/hPX7aDI2m4/
@PG	ID:bammarkduplicates	PN:bammarkduplicates	PP:bamsort	VN:0.0.87	CL:/software/hpag/biobambam/0.0.87/bin/bammarkduplicates I=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/archive/lane2/hPX7aDI2m4/sorted.bam O=/dev/stdout tmpfile=/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/archive/lane2/hPX7aDI2m4/ M=/tmp/M_MEsNARGd level=0
@PG	ID:BamTagStripper	PN:BamTagStripper	PP:bammarkduplicates	DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip	VN:V1.10	CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/dev/stdout TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf51/ILorHSany_sf51/analysis/130906_HS32_10723_B_H722PADXX/Data/Intensities/BAM_basecalls_20130907-084330/PB_cal_bam/archive/lane2/hPX7aDI2m4] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=false CREATE_MD5_FILE=false    QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000
@PG	ID:scramble	PN:scramble	PP:BamTagStripper	VN:1.13.2	CL:/software/badger/bin/scramble -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa 
@SQ	SN:1	LN:249250621	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:1b22b98cdeb4a9304cb5d48026a85128	SP:Homo sapiens
@SQ	SN:2	LN:243199373	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:a0d9851da00400dec1098a9255ac712e	SP:Homo sapiens
@SQ	SN:3	LN:198022430	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:fdfd811849cc2fadebc929bb925902e5	SP:Homo sapiens
@SQ	SN:4	LN:191154276	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:23dccd106897542ad87d2765d28a19a1	SP:Homo sapiens
@SQ	SN:5	LN:180915260	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:0740173db9ffd264d728f32784845cd7	SP:Homo sapiens
@SQ	SN:6	LN:171115067	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:1d3a93a248d92a729ee764823acbbc6b	SP:Homo sapiens
@SQ	SN:7	LN:159138663	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:618366e953d6aaad97dbe4777c29375e	SP:Homo sapiens
@SQ	SN:8	LN:146364022	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:96f514a9929e410c6651697bded59aec	SP:Homo sapiens
@SQ	SN:9	LN:141213431	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:3e273117f15e0a400f01055d9f393768	SP:Homo sapiens
@SQ	SN:10	LN:135534747	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:988c28e000e84c26d552359af1ea2e1d	SP:Homo sapiens
@SQ	SN:11	LN:135006516	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:98c59049a2df285c76ffb1c6db8f8b96	SP:Homo sapiens
@SQ	SN:12	LN:133851895	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:51851ac0e1a115847ad36449b0015864	SP:Homo sapiens
@SQ	SN:13	LN:115169878	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:283f8d7892baa81b510a015719ca7b0b	SP:Homo sapiens
@SQ	SN:14	LN:107349540	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:98f3cae32b2a2e9524bc19813927542e	SP:Homo sapiens
@SQ	SN:15	LN:102531392	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:e5645a794a8238215b2cd77acb95a078	SP:Homo sapiens
@SQ	SN:16	LN:90354753	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:fc9b1a7b42b97a864f56b348b06095e6	SP:Homo sapiens
@SQ	SN:17	LN:81195210	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:351f64d4f4f9ddd45b35336ad97aa6de	SP:Homo sapiens
@SQ	SN:18	LN:78077248	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c	SP:Homo sapiens
@SQ	SN:19	LN:59128983	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:1aacd71f30db8e561810913e0b72636d	SP:Homo sapiens
@SQ	SN:20	LN:63025520	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:0dec9660ec1efaaf33281c0d5ea2560f	SP:Homo sapiens
@SQ	SN:21	LN:48129895	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:2979a6085bfe28e3ad6f552f361ed74d	SP:Homo sapiens
@SQ	SN:22	LN:51304566	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:a718acaa6135fdca8357d5bfe94211dd	SP:Homo sapiens
@SQ	SN:X	LN:155270560	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:7e0e2e580297b7764e31dbc80c2540dd	SP:Homo sapiens
@SQ	SN:Y	LN:59373566	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:1e86411d73e6f00a10590f976be01623	SP:Homo sapiens
@SQ	SN:MT	LN:16569	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa	AS:CGP GRCh37.NCBI.allchr_MT	M5:c68f52674c9fb33aef52dcf399755519	SP:Homo sapiens