@HD	VN:1.0	SO:coordinate
@PG	ID:iSAAC	PN:iSAAC	CL:/illumina/software/Isis/2.6.53.23/Workflows/ResequencingWorker/Isaac/bin/isaac-align --output-directory /scratch/LP2001003-DNA_E01_WFR1869468.c/Analysis/AlignmentTemp/Isaac_LP2001003-DNA_E01/Output --temp-directory /scratch/LP2001003-DNA_E01_WFR1869468.c/Analysis/AlignmentTemp/Isaac_LP2001003-DNA_E01/Temp --bam-gzip-level 6 --scatter-repeats 1 --reference-genome /illumina/software/Isis/Genomes_v4/Homo_sapiens/Ensembl/GRCh37/Sequence/IsaacIndex5/sorted-reference.xml --cleanup-intermediary 1 --memory-limit 123 --clip-semialigned 1 --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 --seed-length 16 --clip-overlapping 1 --bam-exclude-tags none --base-calls /scratch/LP2001003-DNA_E01_WFR1869468.c/RunData/170116_HSX248_0349_AHG2NVALXX/RunInfo.xml --use-bases-mask Y150N1,Y150N1 --tiles s_5_1101,s_5_1102,s_5_1103,s_5_1104,s_5_1105,s_5_1106,s_5_1107,s_5_1108,s_5_1109,s_5_1110,s_5_1111,s_5_1112,s_5_1113,s_5_1114,s_5_1115,s_5_1116,s_5_1117,s_5_1118,s_5_1119,s_5_1120,s_5_1121,s_5_1122,s_5_1123,s_5_1124,s_5_1201,s_5_1202,s_5_1203,s_5_1204,s_5_1205,s_5_1206,s_5_1207,s_5_1208,s_5_1209,s_5_1210,s_5_1211,s_5_1212,s_5_1213,s_5_1214,s_5_1215,s_5_1216,s_5_1217,s_5_1218,s_5_1219,s_5_1220,s_5_1221,s_5_1222,s_5_1223,s_5_1224,s_5_2101,s_5_2102,s_5_2103,s_5_2104,s_5_2105,s_5_2106,s_5_2107,s_5_2108,s_5_2109,s_5_2110,s_5_2112,s_5_2113,s_5_2115,s_5_2116,s_5_2118,s_5_2119,s_5_2120,s_5_2121,s_5_2122,s_5_2124,s_5_2201,s_5_2202,s_5_2203,s_5_2204,s_5_2205,s_5_2206,s_5_2207,s_5_2208,s_5_2209,s_5_2210,s_5_2211,s_5_2212,s_5_2213,s_5_2214,s_5_2215,s_5_2216,s_5_2217,s_5_2218,s_5_2219,s_5_2220,s_5_2221,s_5_2222,s_5_2223,s_5_2224 --base-calls-format bcl-gz -s /scratch/LP2001003-DNA_E01_WFR1869468.c/Analysis/AlignmentTemp/Isaac_LP2001003-DNA_E01/RunFolderInput/FC1.csv --per-tile-tls 0	VN:iSAAC-03.16.02.19
@SQ	SN:1	LN:249250621	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ	SN:2	LN:243199373	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:a0d9851da00400dec1098a9255ac712e
@SQ	SN:3	LN:198022430	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:641e4338fa8d52a5b781bd2a2c08d3c3
@SQ	SN:4	LN:191154276	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:23dccd106897542ad87d2765d28a19a1
@SQ	SN:5	LN:180915260	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:0740173db9ffd264d728f32784845cd7
@SQ	SN:6	LN:171115067	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:1d3a93a248d92a729ee764823acbbc6b
@SQ	SN:7	LN:159138663	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:618366e953d6aaad97dbe4777c29375e
@SQ	SN:8	LN:146364022	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:96f514a9929e410c6651697bded59aec
@SQ	SN:9	LN:141213431	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:3e273117f15e0a400f01055d9f393768
@SQ	SN:10	LN:135534747	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:988c28e000e84c26d552359af1ea2e1d
@SQ	SN:11	LN:135006516	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:98c59049a2df285c76ffb1c6db8f8b96
@SQ	SN:12	LN:133851895	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:51851ac0e1a115847ad36449b0015864
@SQ	SN:13	LN:115169878	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:283f8d7892baa81b510a015719ca7b0b
@SQ	SN:14	LN:107349540	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:98f3cae32b2a2e9524bc19813927542e
@SQ	SN:15	LN:102531392	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:e5645a794a8238215b2cd77acb95a078
@SQ	SN:16	LN:90354753	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:fc9b1a7b42b97a864f56b348b06095e6
@SQ	SN:17	LN:81195210	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:351f64d4f4f9ddd45b35336ad97aa6de
@SQ	SN:18	LN:78077248	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c
@SQ	SN:19	LN:59128983	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:1aacd71f30db8e561810913e0b72636d
@SQ	SN:20	LN:63025520	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:0dec9660ec1efaaf33281c0d5ea2560f
@SQ	SN:21	LN:48129895	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:2979a6085bfe28e3ad6f552f361ed74d
@SQ	SN:22	LN:51304566	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:a718acaa6135fdca8357d5bfe94211dd
@SQ	SN:X	LN:155270560	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:7e0e2e580297b7764e31dbc80c2540dd
@SQ	SN:Y	LN:59373566	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:1fa3474750af0948bdf97d5a0ee52e51
@SQ	SN:MT	LN:16569	UR:/scratch/cbrc/ref/ensembl/human/GRCh37.74/Homo_sapiens.GRCh37.74.dna.fasta	M5:c68f52674c9fb33aef52dcf399755519
@RG	ID:0	PL:ILLUMINA	SM:LP2001003-DNA_E01	PU:HG2NVALXX:5:none