@HD	VN:1.5	SO:coordinate
@SQ	SN:1	LN:249250621	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1b22b98cdeb4a9304cb5d48026a85128	SP:Human
@SQ	SN:2	LN:243199373	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:a0d9851da00400dec1098a9255ac712e	SP:Human
@SQ	SN:3	LN:198022430	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:fdfd811849cc2fadebc929bb925902e5	SP:Human
@SQ	SN:4	LN:191154276	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:23dccd106897542ad87d2765d28a19a1	SP:Human
@SQ	SN:5	LN:180915260	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:0740173db9ffd264d728f32784845cd7	SP:Human
@SQ	SN:6	LN:171115067	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1d3a93a248d92a729ee764823acbbc6b	SP:Human
@SQ	SN:7	LN:159138663	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:618366e953d6aaad97dbe4777c29375e	SP:Human
@SQ	SN:8	LN:146364022	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:96f514a9929e410c6651697bded59aec	SP:Human
@SQ	SN:9	LN:141213431	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:3e273117f15e0a400f01055d9f393768	SP:Human
@SQ	SN:10	LN:135534747	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:988c28e000e84c26d552359af1ea2e1d	SP:Human
@SQ	SN:11	LN:135006516	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:98c59049a2df285c76ffb1c6db8f8b96	SP:Human
@SQ	SN:12	LN:133851895	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:51851ac0e1a115847ad36449b0015864	SP:Human
@SQ	SN:13	LN:115169878	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:283f8d7892baa81b510a015719ca7b0b	SP:Human
@SQ	SN:14	LN:107349540	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:98f3cae32b2a2e9524bc19813927542e	SP:Human
@SQ	SN:15	LN:102531392	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:e5645a794a8238215b2cd77acb95a078	SP:Human
@SQ	SN:16	LN:90354753	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:fc9b1a7b42b97a864f56b348b06095e6	SP:Human
@SQ	SN:17	LN:81195210	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:351f64d4f4f9ddd45b35336ad97aa6de	SP:Human
@SQ	SN:18	LN:78077248	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c	SP:Human
@SQ	SN:19	LN:59128983	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1aacd71f30db8e561810913e0b72636d	SP:Human
@SQ	SN:20	LN:63025520	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:0dec9660ec1efaaf33281c0d5ea2560f	SP:Human
@SQ	SN:21	LN:48129895	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:2979a6085bfe28e3ad6f552f361ed74d	SP:Human
@SQ	SN:22	LN:51304566	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:a718acaa6135fdca8357d5bfe94211dd	SP:Human
@SQ	SN:X	LN:155270560	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:7e0e2e580297b7764e31dbc80c2540dd	SP:Human
@SQ	SN:Y	LN:59373566	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1fa3474750af0948bdf97d5a0ee52e51	SP:Human
@SQ	SN:MT	LN:16569	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:c68f52674c9fb33aef52dcf399755519	SP:Human
@SQ	SN:GL000207.1	LN:4262	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:f3814841f1939d3ca19072d9e89f3fd7	SP:Human
@SQ	SN:GL000226.1	LN:15008	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1c1b2cd1fccbc0a99b6a447fa24d1504	SP:Human
@SQ	SN:GL000229.1	LN:19913	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d0f40ec87de311d8e715b52e4c7062e1	SP:Human
@SQ	SN:GL000231.1	LN:27386	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:ba8882ce3a1efa2080e5d29b956568a4	SP:Human
@SQ	SN:GL000210.1	LN:27682	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:851106a74238044126131ce2a8e5847c	SP:Human
@SQ	SN:GL000239.1	LN:33824	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:99795f15702caec4fa1c4e15f8a29c07	SP:Human
@SQ	SN:GL000235.1	LN:34474	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:118a25ca210cfbcdfb6c2ebb249f9680	SP:Human
@SQ	SN:GL000201.1	LN:36148	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:dfb7e7ec60ffdcb85cb359ea28454ee9	SP:Human
@SQ	SN:GL000247.1	LN:36422	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:7de00226bb7df1c57276ca6baabafd15	SP:Human
@SQ	SN:GL000245.1	LN:36651	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:89bc61960f37d94abf0df2d481ada0ec	SP:Human
@SQ	SN:GL000197.1	LN:37175	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6f5efdd36643a9b8c8ccad6f2f1edc7b	SP:Human
@SQ	SN:GL000203.1	LN:37498	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:96358c325fe0e70bee73436e8bb14dbd	SP:Human
@SQ	SN:GL000246.1	LN:38154	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:e4afcd31912af9d9c2546acf1cb23af2	SP:Human
@SQ	SN:GL000249.1	LN:38502	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1d78abec37c15fe29a275eb08d5af236	SP:Human
@SQ	SN:GL000196.1	LN:38914	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d92206d1bb4c3b4019c43c0875c06dc0	SP:Human
@SQ	SN:GL000248.1	LN:39786	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:5a8e43bec9be36c7b49c84d585107776	SP:Human
@SQ	SN:GL000244.1	LN:39929	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:0996b4475f353ca98bacb756ac479140	SP:Human
@SQ	SN:GL000238.1	LN:39939	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:131b1efc3270cc838686b54e7c34b17b	SP:Human
@SQ	SN:GL000202.1	LN:40103	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:06cbf126247d89664a4faebad130fe9c	SP:Human
@SQ	SN:GL000234.1	LN:40531	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:93f998536b61a56fd0ff47322a911d4b	SP:Human
@SQ	SN:GL000232.1	LN:40652	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:3e06b6741061ad93a8587531307057d8	SP:Human
@SQ	SN:GL000206.1	LN:41001	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:43f69e423533e948bfae5ce1d45bd3f1	SP:Human
@SQ	SN:GL000240.1	LN:41933	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:445a86173da9f237d7bcf41c6cb8cc62	SP:Human
@SQ	SN:GL000236.1	LN:41934	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:fdcd739913efa1fdc64b6c0cd7016779	SP:Human
@SQ	SN:GL000241.1	LN:42152	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:ef4258cdc5a45c206cea8fc3e1d858cf	SP:Human
@SQ	SN:GL000243.1	LN:43341	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:cc34279a7e353136741c9fce79bc4396	SP:Human
@SQ	SN:GL000242.1	LN:43523	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:2f8694fc47576bc81b5fe9e7de0ba49e	SP:Human
@SQ	SN:GL000230.1	LN:43691	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:b4eb71ee878d3706246b7c1dbef69299	SP:Human
@SQ	SN:GL000237.1	LN:45867	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:e0c82e7751df73f4f6d0ed30cdc853c0	SP:Human
@SQ	SN:GL000233.1	LN:45941	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:7fed60298a8d62ff808b74b6ce820001	SP:Human
@SQ	SN:GL000204.1	LN:81310	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:efc49c871536fa8d79cb0a06fa739722	SP:Human
@SQ	SN:GL000198.1	LN:90085	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:868e7784040da90d900d2d1b667a1383	SP:Human
@SQ	SN:GL000208.1	LN:92689	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:aa81be49bf3fe63a79bdc6a6f279abf6	SP:Human
@SQ	SN:GL000191.1	LN:106433	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d75b436f50a8214ee9c2a51d30b2c2cc	SP:Human
@SQ	SN:GL000227.1	LN:128374	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:a4aead23f8053f2655e468bcc6ecdceb	SP:Human
@SQ	SN:GL000228.1	LN:129120	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:c5a17c97e2c1a0b6a9cc5a6b064b714f	SP:Human
@SQ	SN:GL000214.1	LN:137718	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:46c2032c37f2ed899eb41c0473319a69	SP:Human
@SQ	SN:GL000221.1	LN:155397	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:3238fb74ea87ae857f9c7508d315babb	SP:Human
@SQ	SN:GL000209.1	LN:159169	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:f40598e2a5a6b26e84a3775e0d1e2c81	SP:Human
@SQ	SN:GL000218.1	LN:161147	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:1d708b54644c26c7e01c2dad5426d38c	SP:Human
@SQ	SN:GL000220.1	LN:161802	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:fc35de963c57bf7648429e6454f1c9db	SP:Human
@SQ	SN:GL000213.1	LN:164239	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:9d424fdcc98866650b58f004080a992a	SP:Human
@SQ	SN:GL000211.1	LN:166566	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:7daaa45c66b288847b9b32b964e623d3	SP:Human
@SQ	SN:GL000199.1	LN:169874	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:569af3b73522fab4b40995ae4944e78e	SP:Human
@SQ	SN:GL000217.1	LN:172149	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6d243e18dea1945fb7f2517615b8f52e	SP:Human
@SQ	SN:GL000216.1	LN:172294	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:642a232d91c486ac339263820aef7fe0	SP:Human
@SQ	SN:GL000215.1	LN:172545	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:5eb3b418480ae67a997957c909375a73	SP:Human
@SQ	SN:GL000205.1	LN:174588	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d22441398d99caf673e9afb9a1908ec5	SP:Human
@SQ	SN:GL000219.1	LN:179198	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:f977edd13bac459cb2ed4a5457dba1b3	SP:Human
@SQ	SN:GL000224.1	LN:179693	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:d5b2fc04f6b41b212a4198a07f450e20	SP:Human
@SQ	SN:GL000223.1	LN:180455	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:399dfa03bf32022ab52a846f7ca35b30	SP:Human
@SQ	SN:GL000195.1	LN:182896	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:5d9ec007868d517e73543b005ba48535	SP:Human
@SQ	SN:GL000212.1	LN:186858	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:563531689f3dbd691331fd6c5730a88b	SP:Human
@SQ	SN:GL000222.1	LN:186861	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6fe9abac455169f50470f5a6b01d0f59	SP:Human
@SQ	SN:GL000200.1	LN:187035	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:75e4c8d17cd4addf3917d1703cacaf25	SP:Human
@SQ	SN:GL000193.1	LN:189789	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:dbb6e8ece0b5de29da56601613007c2a	SP:Human
@SQ	SN:GL000194.1	LN:191469	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6ac8f815bf8e845bb3031b73f812c012	SP:Human
@SQ	SN:GL000225.1	LN:211173	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:63945c3e6962f28ffd469719a747e73c	SP:Human
@SQ	SN:GL000192.1	LN:547496	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:325ba9e808f669dfeee210fdd7b470ac	SP:Human
@SQ	SN:NC_007605	LN:171823	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:6743bd63b3ff2b5b8985d8933c53290a	SP:Human
@SQ	SN:hs37d5	LN:35477943	UR:/nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa	AS:NCBI37	M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1	SP:Human
@RG	ID:26020_2#4	DT:2018-06-06T00:00:00+0000	PU:180606_HS40_26020_A_HGM2CBCX2_2#4	LB:21701508	PG:SCS	SM:EGAN00001749885	CN:SC	PL:ILLUMINA	DS:EGAS00001002931: This study is a benchmarking exercise to explore potential source of variation between different CRISPR drop out libraries.
@PG	ID:SCS	VN:1.18.66.3	PN:RTA	DS:Controlling software on instrument
@PG	ID:basecalling	PP:SCS	VN:1.18.66.3	PN:RTA	DS:Basecalling Package
@PG	ID:bambi	PP:basecalling	VN:0.11.1	CL:/nfs/gs01/software/pkg/bambi/0.11.1/bin/bambi i2b --intensity-dir=/nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities --basecalls-dir=/nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities/BaseCalls --lane=2 --platform-unit=180606_HS40_26020_A_HGM2CBCX2_2 --read-group-id=26020_2 --study-name="EGAS00001002931: This study is a benchmarking exercise to explore potential source of variation between different CRISPR drop out libraries." --sample-alias=EGAN00001749882,EGAN00001749883,EGAN00001749884,EGAN00001749885,EGAN00001749886,EGAN00001749887 --threads=8 --output-file=- --compression-level=0	PN:bambi	DS:Convert Illumina BCL to BAM or SAM file
@PG	ID:bamadapterfind	PN:bamadapterfind	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bamadapterfind level=0	PP:bambi	VN:2.0.79
@PG	ID:bambi.1	PN:bambi	PP:bamadapterfind	VN:0.11.1	CL:/nfs/gs01/software/pkg/bambi/0.11.1/bin/bambi decode --metrics-file /nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities/BAM_basecalls_20180606-161917/26020_2.bam.tag_decode.metrics --barcode-file /nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities/BAM_basecalls_20180606-161917/metadata_cache_26020/lane_2.taglist --compression-level 0 -
@PG	ID:bamcollate2	PN:bamcollate2	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bamcollate2 collate=2 level=0	PP:bambi.1	VN:2.0.79
@PG	ID:bwa	PN:bwa	CL:/nfs/gs01/software/pkg/bwa/0.7.16a/bwa samse /nfs/gs01/repository/references/PhiX/Sanger-SNPs/all/bwa0_6/phix_unsnipped_short_no_N.fa /tmp/47FfSrZN2c/alnphix_bwa_aln_out /tmp/PeRYngK7RD/alnphix_simple_cat_out	PP:bamcollate2	VN:0.7.16a-r1181
@PG	ID:scramble	PN:scramble	CL:/nfs/gs01/software/pkg/staden_io_lib/1.14.9/bin/scramble -t 5 -0 -I sam -O bam 	PP:bwa	VN:1.14.9
@PG	ID:bam12auxmerge	PN:bam12auxmerge	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/1zqxKw2yfs/simple_cat_out	PP:scramble	VN:2.0.79
@PG	ID:scramble.1	PN:scramble	PP:bam12auxmerge	VN:1.14.9	CL:/nfs/gs01/software/pkg/staden_io_lib/1.14.9/bin/scramble -I bam -O cram -x -3 
@PG	ID:scramble.2	PN:scramble	PP:scramble.1	VN:1.14.9	CL:/nfs/gs01/software/pkg/staden_io_lib/1.14.9/bin/scramble -I cram -O bam -0 
@PG	ID:spf	PN:spatial_filter	PP:scramble.2	DS:A program to apply a spatial filter	VN:0.11.1	CL:/nfs/gs01/software/pkg/bambi/0.11.1/bin/bambi spatial_filter -c -t /nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities/BAM_basecalls_20180606-161917/no_cal/archive/qc/tileviz/26020_2 -F /dev/stdout /dev/stdin ; /nfs/gs01/software/pkg/bambi/0.11.1/bin/bambi spatial_filter -a --compression-level 0 -f -F /tmp/z9ic4VMH86/tee_post_filter_creation:__APPLY_FILTER_OUT___out -l /nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities/BAM_basecalls_20180606-161917/no_cal/26020_2.bam.filter.stats /dev/stdin
@PG	ID:samtools	PN:samtools	PP:spf	VN:1.8	CL:/nfs/gs01/software/pkg/samtools/1.8/bin/samtools split -f /nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities/BAM_basecalls_20180606-161917/no_cal/lane2/%!.bam -
@PG	ID:bamcollate2'	PN:bamcollate2	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bamcollate2 collate=1 level=0	PP:samtools	VN:2.0.79
@PG	ID:bamreset	PN:bamreset	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bamreset resetaux=0 level=0 verbose=0	PP:bamcollate2'	VN:2.0.79
@PG	ID:bamadapterclip	PN:bamadapterclip	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bamadapterclip verbose=0 level=0	PP:bamreset	VN:2.0.79
@PG	ID:bwa'	PN:bwa	CL:/nfs/gs01/software/pkg/bwa/0.7.16a/bwa samse /nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/f8nRLBKF7D/aln_alntgt_bwa_aln_out /tmp/JXPtVloXh1/aln_alntgt_simple_cat_out	PP:bamadapterclip	VN:0.7.16a-r1181
@PG	ID:scramble'	PN:scramble	CL:/nfs/gs01/software/pkg/staden_io_lib/1.14.9/bin/scramble -0 -I sam -O bam 	PP:bwa'	VN:1.14.9
@PG	ID:samtools'	PN:samtools	CL:/nfs/gs01/software/pkg/samtools/1.8/bin/samtools reheader /tmp/_8TqKViLek/aln_postaln_alterSQ_headerSQfix_out /tmp/lCIp7deaH9/aln_postaln_mbuffer_headerSQfix_out	PP:scramble'	VN:1.8
@PG	ID:bam12split	PN:bam12split	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bam12split verbose=0 level=0	PP:samtools'	VN:2.0.79
@PG	ID:bam12auxmerge'	PN:bam12auxmerge	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/Qshu236I_L/aln_amp_bamadapterclip_pre_auxmerge_out	PP:bam12split	VN:2.0.79
@PG	ID:bambi.2	PN:bambi	PP:bam12auxmerge'	VN:0.11.1	CL:/nfs/gs01/software/pkg/bambi/0.11.1/bin/bambi select --compression-level 0 --input /tmp/ODR3z98V9s/aln_tee3_tee3:to_phix_aln_out,/tmp/8OxQGCU4kl/aln_bam12auxmerge_out --output /tmp/AcwG7aRX6S/alignment_filter:phix_bam_out_out,/tmp/cpcBL7x3yu/alignment_filter:target_bam_out_out -m 26020_2#4.bam_alignment_filter_metrics.json	DS:Split alignments into different files
@PG	ID:bamsormadup	PN:bamsormadup	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bamsormadup threads=12 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities/BAM_basecalls_20180606-161917/no_cal/archive/lane2/bsfopt_26020_2#4.tmp	PP:bambi.2	VN:2.0.79
@PG	ID:bamstreamingmarkduplicates	PN:bamstreamingmarkduplicates	CL:/nfs/gs01/software/pkg/biobambam/2.0.79/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities/BAM_basecalls_20180606-161917/no_cal/archive/lane2/bmdfopt_26020_2#4.tmp M=/nfs/gs02/IL_seq_data/analysis/180606_HS40_26020_A_HGM2CBCX2/Data/Intensities/BAM_basecalls_20180606-161917/no_cal/archive/lane2/26020_2#4.markdups_metrics.txt	PP:bamsormadup	VN:2.0.79
@PG	ID:scramble.3	PN:scramble	PP:bamstreamingmarkduplicates	VN:1.14.9	CL:/nfs/gs01/software/pkg/staden_io_lib/1.14.9/bin/scramble -t 5 -7 -I bam -O cram -r /nfs/gs01/repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa 
@CO	TY:checksum	ST:all	PA:all	HA:crc32prod	CO:29586298	BS:c75d0ca	NS:9139e71	SQ:55fab9b	ST:BC,FI,QT,RT,TC:2db05b78
@CO	TY:checksum	ST:all	PA:pass	HA:crc32prod	CO:29586298	BS:c75d0ca	NS:9139e71	SQ:55fab9b	ST:BC,FI,QT,RT,TC:2db05b78
@CO	TY:checksum	ST:	PA:all	HA:crc32prod	CO:0	BS:1	NS:1	SQ:1	ST:BC,FI,QT,RT,TC:1
@CO	TY:checksum	ST:	PA:pass	HA:crc32prod	CO:0	BS:1	NS:1	SQ:1	ST:BC,FI,QT,RT,TC:1
@CO	TY:checksum	ST:26020_2#4	PA:all	HA:crc32prod	CO:29586298	BS:c75d0ca	NS:9139e71	SQ:55fab9b	ST:BC,FI,QT,RT,TC:2db05b78
@CO	TY:checksum	ST:26020_2#4	PA:pass	HA:crc32prod	CO:29586298	BS:c75d0ca	NS:9139e71	SQ:55fab9b	ST:BC,FI,QT,RT,TC:2db05b78