@HD	VN:1.4	SO:coordinate
@RG	ID:1#12	PL:ILLUMINA	PU:140918_HS30_14100_A_C3PL4ACXX_5#12	LB:11455677	DS:EGAS00001000825: Whole exome sequencing of a subset of participants from the INTERVAL study.	DT:2014-09-18T00:00:00+0100	SM:EGAN00001210023	PG:BamIndexDecoder	CN:SC
@PG	ID:SCS	PN:HiSeq Control Software	DS:Controlling software on instrument	VN:2.2.38
@PG	ID:basecalling	PN:RTA	PP:SCS	DS:Basecalling Package	VN:1.18.61.0
@PG	ID:Illumina2bam	PN:Illumina2bam	PP:basecalling	DS:Convert Illumina BCL to BAM or SAM file	VN:V1.16	CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities BASECALLS_DIR=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BaseCalls LANE=5 OUTPUT=/dev/stdout SAMPLE_ALIAS=EGAN00001210012,EGAN00001210013,EGAN00001210014,EGAN00001210015,EGAN00001210016,EGAN00001210017,EGAN00001210018,EGAN00001210019,EGAN00001210020,EGAN00001210021,EGAN00001210022,EGAN00001210023,EGAN00001210024,EGAN00001210025,EGAN00001210026,EGAN00001210027 STUDY_NAME=EGAS00001000825: Whole exome sequencing of a subset of participants from the INTERVAL study. PLATFORM_UNIT=140918_HS30_14100_A_C3PL4ACXX_5 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:0.0.163	CL:bamadapterfind level=0
@PG	ID:BamIndexDecoder	PN:BamIndexDecoder	PP:bamadapterfind	DS:A command-line tool to decode multiplexed bam file	VN:V1.16	CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/14100_5.bam BARCODE_FILE=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/lane_5.taglist METRICS_FILE=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/14100_5.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:v10.18	CL:/software/solexa/pkg/pb_calibration/v10.18/bin/spatial_filter -c  -F pb_align_14100_5.bam.filter -t /nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/archive/qc/tileviz/14100_5 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_14100_5.bam ; /software/solexa/pkg/pb_calibration/v10.18/bin/spatial_filter -a  -f  -u  -F pb_align_14100_5.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:V1.16	CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_14100_5.bam INPUT=/dev/stdin OUTPUT=14100_5.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:V1.16	CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/14100_5.bam OUTPUT_PREFIX=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/lane5/14100_5 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/pkg/bwa/bwa-0.5.10-mt_fixes/bwa aln -q 15 -t 12 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa/hs37d5.fa -b1 /nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/lane5/14100_5#12.bam > /tmp/1JmrJAS63B/1.sai
@PG	ID:bwa_aln_1	PN:bwa	PP:bwa_aln	VN:0.5.10-tpx	CL:/software/solexa/pkg/bwa/bwa-0.5.10-mt_fixes/bwa aln -q 15 -t 12 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa/hs37d5.fa -b2 /nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/lane5/14100_5#12.bam > /tmp/1JmrJAS63B/2.sai
@PG	ID:bwa_sam	PN:bwa	PP:bwa_aln_1	VN:0.5.10-tpx	CL:/software/solexa/pkg/bwa/bwa-0.5.10-mt_fixes/bwa sampe -t 6 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa/hs37d5.fa /tmp/1JmrJAS63B/1.sai /tmp/1JmrJAS63B/2.sai /nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/lane5/14100_5#12.bam /nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/lane5/14100_5#12.bam
@PG	ID:Picard_SamFormatConverter	PN:SamFormatConverter	PP:bwa_sam	VN:1.72(1230)	CL:/software/jdk1.7.0_25/bin/java -Xmx1000m -jar /software/solexa/pkg/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/pkg/samtools/samtools-0.1.18/samtools fixmate - -
@PG	ID:BamMerger_1	PN:BamMerger	PP:samtools_fixmate	VN:V1.16	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/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/lane5/14100_5#12.bam OUTPUT=/tmp/1JmrJAS63B/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:V1.16	CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/lane5/14100_5#12.bam, /tmp/1JmrJAS63B/output_fifo.bam] OUTPUT_ALIGNMENT=[/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/archive/lane5/14100_5#12_phix.bam, /nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/archive/lane5/14100_5#12.bam] METRICS_FILE=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/archive/lane5/14100_5#12.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:0.0.163	CL:/software/hpag/biobambam/0.0.163/bin/bamsort tmpfile=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/archive/lane5/kBsMD_YGgI/
@PG	ID:bammarkduplicates	PN:bammarkduplicates	PP:bamsort	VN:0.0.163	CL:/software/hpag/biobambam/0.0.163/bin/bammarkduplicates I=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/archive/lane5/kBsMD_YGgI/sorted.bam O=/dev/stdout tmpfile=/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/archive/lane5/kBsMD_YGgI/ M=/tmp/QFcbWp6i2Z 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:V1.16	CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/dev/stdout TAG_TO_KEEP=[a3, aa, af, ah, as, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf50/ILorHSany_sf50/analysis/140918_HS30_14100_A_C3PL4ACXX/Data/Intensities/BAM_basecalls_20140927-020158/no_cal/archive/lane5/kBsMD_YGgI] 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:1.13.5	CL:/software/badger/bin/scramble -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa 
@SQ	SN:1	LN:249250621	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1b22b98cdeb4a9304cb5d48026a85128	SP:Human
@SQ	SN:2	LN:243199373	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:a0d9851da00400dec1098a9255ac712e	SP:Human
@SQ	SN:3	LN:198022430	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:fdfd811849cc2fadebc929bb925902e5	SP:Human
@SQ	SN:4	LN:191154276	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:23dccd106897542ad87d2765d28a19a1	SP:Human
@SQ	SN:5	LN:180915260	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:0740173db9ffd264d728f32784845cd7	SP:Human
@SQ	SN:6	LN:171115067	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1d3a93a248d92a729ee764823acbbc6b	SP:Human
@SQ	SN:7	LN:159138663	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:618366e953d6aaad97dbe4777c29375e	SP:Human
@SQ	SN:8	LN:146364022	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:96f514a9929e410c6651697bded59aec	SP:Human
@SQ	SN:9	LN:141213431	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:3e273117f15e0a400f01055d9f393768	SP:Human
@SQ	SN:10	LN:135534747	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:988c28e000e84c26d552359af1ea2e1d	SP:Human
@SQ	SN:11	LN:135006516	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:98c59049a2df285c76ffb1c6db8f8b96	SP:Human
@SQ	SN:12	LN:133851895	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:51851ac0e1a115847ad36449b0015864	SP:Human
@SQ	SN:13	LN:115169878	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:283f8d7892baa81b510a015719ca7b0b	SP:Human
@SQ	SN:14	LN:107349540	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:98f3cae32b2a2e9524bc19813927542e	SP:Human
@SQ	SN:15	LN:102531392	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:e5645a794a8238215b2cd77acb95a078	SP:Human
@SQ	SN:16	LN:90354753	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:fc9b1a7b42b97a864f56b348b06095e6	SP:Human
@SQ	SN:17	LN:81195210	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:351f64d4f4f9ddd45b35336ad97aa6de	SP:Human
@SQ	SN:18	LN:78077248	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c	SP:Human
@SQ	SN:19	LN:59128983	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1aacd71f30db8e561810913e0b72636d	SP:Human
@SQ	SN:20	LN:63025520	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:0dec9660ec1efaaf33281c0d5ea2560f	SP:Human
@SQ	SN:21	LN:48129895	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:2979a6085bfe28e3ad6f552f361ed74d	SP:Human
@SQ	SN:22	LN:51304566	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:a718acaa6135fdca8357d5bfe94211dd	SP:Human
@SQ	SN:X	LN:155270560	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:7e0e2e580297b7764e31dbc80c2540dd	SP:Human
@SQ	SN:Y	LN:59373566	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1fa3474750af0948bdf97d5a0ee52e51	SP:Human
@SQ	SN:MT	LN:16569	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:c68f52674c9fb33aef52dcf399755519	SP:Human
@SQ	SN:GL000207.1	LN:4262	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:f3814841f1939d3ca19072d9e89f3fd7	SP:Human
@SQ	SN:GL000226.1	LN:15008	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1c1b2cd1fccbc0a99b6a447fa24d1504	SP:Human
@SQ	SN:GL000229.1	LN:19913	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d0f40ec87de311d8e715b52e4c7062e1	SP:Human
@SQ	SN:GL000231.1	LN:27386	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:ba8882ce3a1efa2080e5d29b956568a4	SP:Human
@SQ	SN:GL000210.1	LN:27682	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:851106a74238044126131ce2a8e5847c	SP:Human
@SQ	SN:GL000239.1	LN:33824	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:99795f15702caec4fa1c4e15f8a29c07	SP:Human
@SQ	SN:GL000235.1	LN:34474	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:118a25ca210cfbcdfb6c2ebb249f9680	SP:Human
@SQ	SN:GL000201.1	LN:36148	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:dfb7e7ec60ffdcb85cb359ea28454ee9	SP:Human
@SQ	SN:GL000247.1	LN:36422	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:7de00226bb7df1c57276ca6baabafd15	SP:Human
@SQ	SN:GL000245.1	LN:36651	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:89bc61960f37d94abf0df2d481ada0ec	SP:Human
@SQ	SN:GL000197.1	LN:37175	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6f5efdd36643a9b8c8ccad6f2f1edc7b	SP:Human
@SQ	SN:GL000203.1	LN:37498	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:96358c325fe0e70bee73436e8bb14dbd	SP:Human
@SQ	SN:GL000246.1	LN:38154	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:e4afcd31912af9d9c2546acf1cb23af2	SP:Human
@SQ	SN:GL000249.1	LN:38502	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1d78abec37c15fe29a275eb08d5af236	SP:Human
@SQ	SN:GL000196.1	LN:38914	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d92206d1bb4c3b4019c43c0875c06dc0	SP:Human
@SQ	SN:GL000248.1	LN:39786	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:5a8e43bec9be36c7b49c84d585107776	SP:Human
@SQ	SN:GL000244.1	LN:39929	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:0996b4475f353ca98bacb756ac479140	SP:Human
@SQ	SN:GL000238.1	LN:39939	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:131b1efc3270cc838686b54e7c34b17b	SP:Human
@SQ	SN:GL000202.1	LN:40103	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:06cbf126247d89664a4faebad130fe9c	SP:Human
@SQ	SN:GL000234.1	LN:40531	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:93f998536b61a56fd0ff47322a911d4b	SP:Human
@SQ	SN:GL000232.1	LN:40652	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:3e06b6741061ad93a8587531307057d8	SP:Human
@SQ	SN:GL000206.1	LN:41001	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:43f69e423533e948bfae5ce1d45bd3f1	SP:Human
@SQ	SN:GL000240.1	LN:41933	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:445a86173da9f237d7bcf41c6cb8cc62	SP:Human
@SQ	SN:GL000236.1	LN:41934	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:fdcd739913efa1fdc64b6c0cd7016779	SP:Human
@SQ	SN:GL000241.1	LN:42152	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:ef4258cdc5a45c206cea8fc3e1d858cf	SP:Human
@SQ	SN:GL000243.1	LN:43341	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:cc34279a7e353136741c9fce79bc4396	SP:Human
@SQ	SN:GL000242.1	LN:43523	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:2f8694fc47576bc81b5fe9e7de0ba49e	SP:Human
@SQ	SN:GL000230.1	LN:43691	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:b4eb71ee878d3706246b7c1dbef69299	SP:Human
@SQ	SN:GL000237.1	LN:45867	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:e0c82e7751df73f4f6d0ed30cdc853c0	SP:Human
@SQ	SN:GL000233.1	LN:45941	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:7fed60298a8d62ff808b74b6ce820001	SP:Human
@SQ	SN:GL000204.1	LN:81310	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:efc49c871536fa8d79cb0a06fa739722	SP:Human
@SQ	SN:GL000198.1	LN:90085	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:868e7784040da90d900d2d1b667a1383	SP:Human
@SQ	SN:GL000208.1	LN:92689	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:aa81be49bf3fe63a79bdc6a6f279abf6	SP:Human
@SQ	SN:GL000191.1	LN:106433	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d75b436f50a8214ee9c2a51d30b2c2cc	SP:Human
@SQ	SN:GL000227.1	LN:128374	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:a4aead23f8053f2655e468bcc6ecdceb	SP:Human
@SQ	SN:GL000228.1	LN:129120	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:c5a17c97e2c1a0b6a9cc5a6b064b714f	SP:Human
@SQ	SN:GL000214.1	LN:137718	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:46c2032c37f2ed899eb41c0473319a69	SP:Human
@SQ	SN:GL000221.1	LN:155397	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:3238fb74ea87ae857f9c7508d315babb	SP:Human
@SQ	SN:GL000209.1	LN:159169	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:f40598e2a5a6b26e84a3775e0d1e2c81	SP:Human
@SQ	SN:GL000218.1	LN:161147	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1d708b54644c26c7e01c2dad5426d38c	SP:Human
@SQ	SN:GL000220.1	LN:161802	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:fc35de963c57bf7648429e6454f1c9db	SP:Human
@SQ	SN:GL000213.1	LN:164239	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:9d424fdcc98866650b58f004080a992a	SP:Human
@SQ	SN:GL000211.1	LN:166566	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:7daaa45c66b288847b9b32b964e623d3	SP:Human
@SQ	SN:GL000199.1	LN:169874	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:569af3b73522fab4b40995ae4944e78e	SP:Human
@SQ	SN:GL000217.1	LN:172149	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6d243e18dea1945fb7f2517615b8f52e	SP:Human
@SQ	SN:GL000216.1	LN:172294	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:642a232d91c486ac339263820aef7fe0	SP:Human
@SQ	SN:GL000215.1	LN:172545	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:5eb3b418480ae67a997957c909375a73	SP:Human
@SQ	SN:GL000205.1	LN:174588	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d22441398d99caf673e9afb9a1908ec5	SP:Human
@SQ	SN:GL000219.1	LN:179198	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:f977edd13bac459cb2ed4a5457dba1b3	SP:Human
@SQ	SN:GL000224.1	LN:179693	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d5b2fc04f6b41b212a4198a07f450e20	SP:Human
@SQ	SN:GL000223.1	LN:180455	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:399dfa03bf32022ab52a846f7ca35b30	SP:Human
@SQ	SN:GL000195.1	LN:182896	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:5d9ec007868d517e73543b005ba48535	SP:Human
@SQ	SN:GL000212.1	LN:186858	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:563531689f3dbd691331fd6c5730a88b	SP:Human
@SQ	SN:GL000222.1	LN:186861	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6fe9abac455169f50470f5a6b01d0f59	SP:Human
@SQ	SN:GL000200.1	LN:187035	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:75e4c8d17cd4addf3917d1703cacaf25	SP:Human
@SQ	SN:GL000193.1	LN:189789	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:dbb6e8ece0b5de29da56601613007c2a	SP:Human
@SQ	SN:GL000194.1	LN:191469	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6ac8f815bf8e845bb3031b73f812c012	SP:Human
@SQ	SN:GL000225.1	LN:211173	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:63945c3e6962f28ffd469719a747e73c	SP:Human
@SQ	SN:GL000192.1	LN:547496	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:325ba9e808f669dfeee210fdd7b470ac	SP:Human
@SQ	SN:NC_007605	LN:171823	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6743bd63b3ff2b5b8985d8933c53290a	SP:Human
@SQ	SN:hs37d5	LN:35477943	UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1	SP:Human