@HD	VN:1.0	GO:none	SO:coordinate
@RG	ID:0	PL:ILLUMINA	PU:C3Y02ACXX_0:1:none	SM:LP6005876-DNA_B08
@RG	ID:1	PL:ILLUMINA	PU:C3Y02ACXX_0:2:none	SM:LP6005876-DNA_B08
@RG	ID:2	PL:ILLUMINA	PU:C3Y02ACXX_0:3:none	SM:LP6005876-DNA_B08
@SQ	SN:chrM	LN:16571	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:d2ed829b8a1628d16cbeee88e88e39eb
@SQ	SN:chr1	LN:249250621	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ	SN:chr2	LN:243199373	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:a0d9851da00400dec1098a9255ac712e
@SQ	SN:chr3	LN:198022430	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:641e4338fa8d52a5b781bd2a2c08d3c3
@SQ	SN:chr4	LN:191154276	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:23dccd106897542ad87d2765d28a19a1
@SQ	SN:chr5	LN:180915260	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:0740173db9ffd264d728f32784845cd7
@SQ	SN:chr6	LN:171115067	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:1d3a93a248d92a729ee764823acbbc6b
@SQ	SN:chr7	LN:159138663	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:618366e953d6aaad97dbe4777c29375e
@SQ	SN:chr8	LN:146364022	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:96f514a9929e410c6651697bded59aec
@SQ	SN:chr9	LN:141213431	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:3e273117f15e0a400f01055d9f393768
@SQ	SN:chr10	LN:135534747	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:988c28e000e84c26d552359af1ea2e1d
@SQ	SN:chr11	LN:135006516	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:98c59049a2df285c76ffb1c6db8f8b96
@SQ	SN:chr12	LN:133851895	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:51851ac0e1a115847ad36449b0015864
@SQ	SN:chr13	LN:115169878	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:283f8d7892baa81b510a015719ca7b0b
@SQ	SN:chr14	LN:107349540	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:98f3cae32b2a2e9524bc19813927542e
@SQ	SN:chr15	LN:102531392	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:e5645a794a8238215b2cd77acb95a078
@SQ	SN:chr16	LN:90354753	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:fc9b1a7b42b97a864f56b348b06095e6
@SQ	SN:chr17	LN:81195210	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:351f64d4f4f9ddd45b35336ad97aa6de
@SQ	SN:chr18	LN:78077248	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c
@SQ	SN:chr19	LN:59128983	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:1aacd71f30db8e561810913e0b72636d
@SQ	SN:chr20	LN:63025520	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:0dec9660ec1efaaf33281c0d5ea2560f
@SQ	SN:chr21	LN:48129895	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:2979a6085bfe28e3ad6f552f361ed74d
@SQ	SN:chr22	LN:51304566	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:a718acaa6135fdca8357d5bfe94211dd
@SQ	SN:chrX	LN:155270560	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:7e0e2e580297b7764e31dbc80c2540dd
@SQ	SN:chrY	LN:59373566	UR:/cvmfs/softdrive.nl/projectmine_sw/resources/Build37/hg19/ucsc.hg19.fasta	M5:1fa3474750af0948bdf97d5a0ee52e51
@PG	ID:iSAAC	PN:iSAAC	VN:iSAAC-01.13.04.29	CL:/illumina/development/Isis/2.3.23.1/Workflows/ResequencingWorker/isaac-align --qscore-bin 1 --stop-at Bam --reference-genome /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/IsaacIndex/sorted-reference.xml --memory-limit 122 --output-directory /scratch/LP6005876-DNA_B08_WF40488/Alignment/IsaacAlignment --temp-directory /scratch/LP6005876-DNA_B08_WF40488/Alignment/IsaacTemp --base-quality-cutoff 15 --pf-only 1 --gap-scoring bwa --keep-duplicates 1 --keep-unaligned back --stats-image-format none --variable-fastq-read-length yes --ignore-missing-bcls 1 --ignore-missing-filters 1 --realign-gaps no --base-calls-directory /scratch/LP6005876-DNA_B08_WF40488/RunData/140417_SN589_0245_BC3Y02ACXX_sd-seq/Data/Intensities/BaseCalls --barcode-mismatches 1 --use-bases-mask Y100n,Y100n --tiles s_1,s_2,s_3 --base-calls-format bcl-gz -s /scratch/LP6005876-DNA_B08_WF40488/Alignment/tmp.0.0.dat
@PG	ID:GATK IndelRealigner	VN:1.6-22-g3ec78bd	CL:knownAlleles=[] targetIntervals=/scratch/LP6005876-DNA_B08_WF40488/Alignment/LP6005876-DNA-B08_S1_chrM.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:Illumina_WGS_Services	VN:v2.0.2