@HD	VN:1.0	SO:coordinate
@PG	ID:iSAAC	PN:iSAAC	CL:/illumina/software/Isis/2.5.55.16.NorthStar/Workflows/ResequencingWorker/isaac-align --bam-exclude-tags=none --bam-gzip-level 6 --lane-number-max 8 --bam-header-tag @PG\tID:Illumina_WGS_Gel\tVN:v4.0.0 --reference-genome /fixtures/Genomes/Homo_sapiens/Ensembl/GRCh37/Sequence/IsaacIndex3/sorted-reference.xml --cleanup-intermediary 1 --memory-limit 123 --output-directory /scratch/LP2000879-DNA_F07_WFR437961/Alignment/IsaacAlignment --temp-directory /scratch/LP2000879-DNA_F07_WFR437961/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/LP2000879-DNA_F07_WFR437961/RunData/160215_HSX1102_0254_AHKMJTCCXX/RunInfo.xml --barcode-mismatches 1 --use-bases-mask Y150N1,Y150N1 --tiles s_6_1101,s_6_1102,s_6_1103,s_6_1104,s_6_1105,s_6_1106,s_6_1107,s_6_1108,s_6_1109,s_6_1110,s_6_1111,s_6_1112,s_6_1113,s_6_1114,s_6_1115,s_6_1116,s_6_1117,s_6_1118,s_6_1119,s_6_1120,s_6_1121,s_6_1122,s_6_1123,s_6_1124,s_6_1201,s_6_1202,s_6_1203,s_6_1204,s_6_1205,s_6_1206,s_6_1207,s_6_1208,s_6_1209,s_6_1210,s_6_1211,s_6_1212,s_6_1213,s_6_1214,s_6_1215,s_6_1216,s_6_1217,s_6_1218,s_6_1219,s_6_1220,s_6_1221,s_6_1222,s_6_1223,s_6_1224,s_6_2101,s_6_2102,s_6_2103,s_6_2104,s_6_2105,s_6_2106,s_6_2107,s_6_2108,s_6_2109,s_6_2110,s_6_2111,s_6_2112,s_6_2113,s_6_2114,s_6_2115,s_6_2116,s_6_2117,s_6_2118,s_6_2119,s_6_2120,s_6_2121,s_6_2122,s_6_2123,s_6_2124,s_6_2201,s_6_2202,s_6_2203,s_6_2204,s_6_2205,s_6_2207,s_6_2208,s_6_2209,s_6_2210,s_6_2211,s_6_2212,s_6_2213,s_6_2214,s_6_2215,s_6_2216,s_6_2217,s_6_2218,s_6_2219,s_6_2220,s_6_2221,s_6_2222,s_6_2223,s_6_2224 --base-calls-format bcl-gz -s /scratch/LP2000879-DNA_F07_WFR437961/Alignment/tmp.0.0.dat --clip-overlapping 1	VN:iSAAC-SAAC00776.15.01.27
@PG	ID:Illumina_WGS_Gel	VN:v4.0.0
@SQ	SN:1	LN:249250621	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ	SN:2	LN:243199373	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:a0d9851da00400dec1098a9255ac712e
@SQ	SN:3	LN:198022430	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:fdfd811849cc2fadebc929bb925902e5
@SQ	SN:4	LN:191154276	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:23dccd106897542ad87d2765d28a19a1
@SQ	SN:5	LN:180915260	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:0740173db9ffd264d728f32784845cd7
@SQ	SN:6	LN:171115067	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:1d3a93a248d92a729ee764823acbbc6b
@SQ	SN:7	LN:159138663	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:618366e953d6aaad97dbe4777c29375e
@SQ	SN:8	LN:146364022	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:96f514a9929e410c6651697bded59aec
@SQ	SN:9	LN:141213431	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:3e273117f15e0a400f01055d9f393768
@SQ	SN:10	LN:135534747	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:988c28e000e84c26d552359af1ea2e1d
@SQ	SN:11	LN:135006516	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:98c59049a2df285c76ffb1c6db8f8b96
@SQ	SN:12	LN:133851895	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:51851ac0e1a115847ad36449b0015864
@SQ	SN:13	LN:115169878	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:283f8d7892baa81b510a015719ca7b0b
@SQ	SN:14	LN:107349540	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:98f3cae32b2a2e9524bc19813927542e
@SQ	SN:15	LN:102531392	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:e5645a794a8238215b2cd77acb95a078
@SQ	SN:16	LN:90354753	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:fc9b1a7b42b97a864f56b348b06095e6
@SQ	SN:17	LN:81195210	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:351f64d4f4f9ddd45b35336ad97aa6de
@SQ	SN:18	LN:78077248	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c
@SQ	SN:19	LN:59128983	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:1aacd71f30db8e561810913e0b72636d
@SQ	SN:20	LN:63025520	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:0dec9660ec1efaaf33281c0d5ea2560f
@SQ	SN:21	LN:48129895	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:2979a6085bfe28e3ad6f552f361ed74d
@SQ	SN:22	LN:51304566	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:a718acaa6135fdca8357d5bfe94211dd
@SQ	SN:X	LN:155270560	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:7e0e2e580297b7764e31dbc80c2540dd
@SQ	SN:Y	LN:59373566	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:1fa3474750af0948bdf97d5a0ee52e51
@SQ	SN:MT	LN:16569	UR:/scratch/cbrc/ref/broad_bundle_b37_2.8/human_g1k_v37_primary.fasta	M5:c68f52674c9fb33aef52dcf399755519
@RG	ID:0	PL:ILLUMINA	SM:LP2000879-DNA_F07	PU:HKMJTCCXX:6:none