@HD	VN:1.0	SO:coordinate
@PG	ID:iSAAC	PN:iSAAC	CL:/illumina/development/Isas/2.5.55.16.NorthStar/Workflows/ResequencingWorker/isaac-align --qscore-bin 1 --bam-exclude-tags=none --bam-gzip-level 6 --lane-number-max 8 --bam-header-tag @PG\tID:Illumina_WGS_Services\tVN:v4.0.3 --reference-genome /illumina/sync/software/unofficial/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/IsaacIndex3/sorted-reference.xml --cleanup-intermediary 1 --memory-limit 123 --output-directory /scratch/LP6008190-DNA_E12_WFR1168494/Alignment/IsaacAlignment --temp-directory /scratch/LP6008190-DNA_E12_WFR1168494/Alignment/IsaacTemp --base-quality-cutoff 15 --stats-image-format none --gap-scoring bwa --variable-read-length yes --ignore-missing-bcls 1 --ignore-missing-filters 1 --split-gap-length 10000 --per-tile-tls 1 --seed-length 32 -b /scratch/LP6008190-DNA_E12_WFR1168494/RunData/160208_1267_0000_AHKGGCCCXX_LR/RunInfo.xml --barcode-mismatches 1 --use-bases-mask Y150N1,Y150N1 --tiles s_8_1101,s_8_1102,s_8_1103,s_8_1104,s_8_1105,s_8_1106,s_8_1107,s_8_1108,s_8_1109,s_8_1110,s_8_1111,s_8_1112,s_8_1113,s_8_1114,s_8_1115,s_8_1116,s_8_1117,s_8_1118,s_8_1119,s_8_1120,s_8_1121,s_8_1122,s_8_1123,s_8_1124,s_8_1201,s_8_1202,s_8_1203,s_8_1204,s_8_1205,s_8_1206,s_8_1207,s_8_1208,s_8_1209,s_8_1210,s_8_1211,s_8_1212,s_8_1213,s_8_1214,s_8_1215,s_8_1216,s_8_1217,s_8_1218,s_8_1219,s_8_1220,s_8_1221,s_8_1222,s_8_1223,s_8_1224,s_8_2101,s_8_2102,s_8_2103,s_8_2104,s_8_2105,s_8_2106,s_8_2107,s_8_2108,s_8_2109,s_8_2110,s_8_2111,s_8_2112,s_8_2113,s_8_2114,s_8_2115,s_8_2116,s_8_2117,s_8_2118,s_8_2119,s_8_2120,s_8_2121,s_8_2122,s_8_2123,s_8_2124,s_8_2201,s_8_2202,s_8_2203,s_8_2204,s_8_2205,s_8_2206,s_8_2207,s_8_2208,s_8_2209,s_8_2210,s_8_2211,s_8_2213,s_8_2214,s_8_2216,s_8_2218,s_8_2219,s_8_2221,s_8_2222,s_8_2223,s_8_2224 --base-calls-format bcl-gz -s /scratch/LP6008190-DNA_E12_WFR1168494/Alignment/tmp.0.0.dat -b /scratch/LP6008190-DNA_E12_WFR1168494/RunData/160211_315_0209_BHKK3KCCXX_ReQ_160210_1_su/RunInfo.xml --barcode-mismatches 1 --use-bases-mask Y150N1,Y150N1 --tiles s_4 --base-calls-format bcl-gz -s /scratch/LP6008190-DNA_E12_WFR1168494/Alignment/tmp.1.0.dat --clip-overlapping 1	VN:iSAAC-SAAC00776.15.01.27
@PG	ID:Illumina_WGS_Services	VN:v4.0.3
@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
@RG	ID:0	PL:ILLUMINA	SM:LP6008190-DNA_E12	PU:HKGGCCCXX:8:none
@RG	ID:1	PL:ILLUMINA	SM:LP6008190-DNA_E12	PU:HKK3KCCXX:4:none