@HD VN:1.4 SO:coordinate @SQ SN:1 LN:249250621 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Human @SQ SN:2 LN:243199373 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:a0d9851da00400dec1098a9255ac712e SP:Human @SQ SN:3 LN:198022430 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:fdfd811849cc2fadebc929bb925902e5 SP:Human @SQ SN:4 LN:191154276 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:23dccd106897542ad87d2765d28a19a1 SP:Human @SQ SN:5 LN:180915260 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:0740173db9ffd264d728f32784845cd7 SP:Human @SQ SN:6 LN:171115067 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1d3a93a248d92a729ee764823acbbc6b SP:Human @SQ SN:7 LN:159138663 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:618366e953d6aaad97dbe4777c29375e SP:Human @SQ SN:8 LN:146364022 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:96f514a9929e410c6651697bded59aec SP:Human @SQ SN:9 LN:141213431 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:3e273117f15e0a400f01055d9f393768 SP:Human @SQ SN:10 LN:135534747 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:988c28e000e84c26d552359af1ea2e1d SP:Human @SQ SN:11 LN:135006516 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Human @SQ SN:12 LN:133851895 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:51851ac0e1a115847ad36449b0015864 SP:Human @SQ SN:13 LN:115169878 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:283f8d7892baa81b510a015719ca7b0b SP:Human @SQ SN:14 LN:107349540 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:98f3cae32b2a2e9524bc19813927542e SP:Human @SQ SN:15 LN:102531392 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:e5645a794a8238215b2cd77acb95a078 SP:Human @SQ SN:16 LN:90354753 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Human @SQ SN:17 LN:81195210 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Human @SQ SN:18 LN:78077248 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Human @SQ SN:19 LN:59128983 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1aacd71f30db8e561810913e0b72636d SP:Human @SQ SN:20 LN:63025520 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Human @SQ SN:21 LN:48129895 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:2979a6085bfe28e3ad6f552f361ed74d SP:Human @SQ SN:22 LN:51304566 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:a718acaa6135fdca8357d5bfe94211dd SP:Human @SQ SN:X LN:155270560 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:7e0e2e580297b7764e31dbc80c2540dd SP:Human @SQ SN:Y LN:59373566 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Human @SQ SN:MT LN:16569 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:c68f52674c9fb33aef52dcf399755519 SP:Human @SQ SN:GL000207.1 LN:4262 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Human @SQ SN:GL000226.1 LN:15008 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Human @SQ SN:GL000229.1 LN:19913 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Human @SQ SN:GL000231.1 LN:27386 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Human @SQ SN:GL000210.1 LN:27682 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:851106a74238044126131ce2a8e5847c SP:Human @SQ SN:GL000239.1 LN:33824 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:99795f15702caec4fa1c4e15f8a29c07 SP:Human @SQ SN:GL000235.1 LN:34474 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Human @SQ SN:GL000201.1 LN:36148 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Human @SQ SN:GL000247.1 LN:36422 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:7de00226bb7df1c57276ca6baabafd15 SP:Human @SQ SN:GL000245.1 LN:36651 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:89bc61960f37d94abf0df2d481ada0ec SP:Human @SQ SN:GL000197.1 LN:37175 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Human @SQ SN:GL000203.1 LN:37498 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:96358c325fe0e70bee73436e8bb14dbd SP:Human @SQ SN:GL000246.1 LN:38154 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Human @SQ SN:GL000249.1 LN:38502 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1d78abec37c15fe29a275eb08d5af236 SP:Human @SQ SN:GL000196.1 LN:38914 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Human @SQ SN:GL000248.1 LN:39786 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:5a8e43bec9be36c7b49c84d585107776 SP:Human @SQ SN:GL000244.1 LN:39929 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:0996b4475f353ca98bacb756ac479140 SP:Human @SQ SN:GL000238.1 LN:39939 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:131b1efc3270cc838686b54e7c34b17b SP:Human @SQ SN:GL000202.1 LN:40103 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:06cbf126247d89664a4faebad130fe9c SP:Human @SQ SN:GL000234.1 LN:40531 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:93f998536b61a56fd0ff47322a911d4b SP:Human @SQ SN:GL000232.1 LN:40652 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:3e06b6741061ad93a8587531307057d8 SP:Human @SQ SN:GL000206.1 LN:41001 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Human @SQ SN:GL000240.1 LN:41933 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Human @SQ SN:GL000236.1 LN:41934 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Human @SQ SN:GL000241.1 LN:42152 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Human @SQ SN:GL000243.1 LN:43341 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:cc34279a7e353136741c9fce79bc4396 SP:Human @SQ SN:GL000242.1 LN:43523 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Human @SQ SN:GL000230.1 LN:43691 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:b4eb71ee878d3706246b7c1dbef69299 SP:Human @SQ SN:GL000237.1 LN:45867 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Human @SQ SN:GL000233.1 LN:45941 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:7fed60298a8d62ff808b74b6ce820001 SP:Human @SQ SN:GL000204.1 LN:81310 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:efc49c871536fa8d79cb0a06fa739722 SP:Human @SQ SN:GL000198.1 LN:90085 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:868e7784040da90d900d2d1b667a1383 SP:Human @SQ SN:GL000208.1 LN:92689 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Human @SQ SN:GL000191.1 LN:106433 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Human @SQ SN:GL000227.1 LN:128374 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:a4aead23f8053f2655e468bcc6ecdceb SP:Human @SQ SN:GL000228.1 LN:129120 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Human @SQ SN:GL000214.1 LN:137718 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:46c2032c37f2ed899eb41c0473319a69 SP:Human @SQ SN:GL000221.1 LN:155397 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:3238fb74ea87ae857f9c7508d315babb SP:Human @SQ SN:GL000209.1 LN:159169 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Human @SQ SN:GL000218.1 LN:161147 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1d708b54644c26c7e01c2dad5426d38c SP:Human @SQ SN:GL000220.1 LN:161802 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:fc35de963c57bf7648429e6454f1c9db SP:Human @SQ SN:GL000213.1 LN:164239 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:9d424fdcc98866650b58f004080a992a SP:Human @SQ SN:GL000211.1 LN:166566 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:7daaa45c66b288847b9b32b964e623d3 SP:Human @SQ SN:GL000199.1 LN:169874 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:569af3b73522fab4b40995ae4944e78e SP:Human @SQ SN:GL000217.1 LN:172149 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:6d243e18dea1945fb7f2517615b8f52e SP:Human @SQ SN:GL000216.1 LN:172294 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:642a232d91c486ac339263820aef7fe0 SP:Human @SQ SN:GL000215.1 LN:172545 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:5eb3b418480ae67a997957c909375a73 SP:Human @SQ SN:GL000205.1 LN:174588 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d22441398d99caf673e9afb9a1908ec5 SP:Human @SQ SN:GL000219.1 LN:179198 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Human @SQ SN:GL000224.1 LN:179693 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Human @SQ SN:GL000223.1 LN:180455 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Human @SQ SN:GL000195.1 LN:182896 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:5d9ec007868d517e73543b005ba48535 SP:Human @SQ SN:GL000212.1 LN:186858 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:563531689f3dbd691331fd6c5730a88b SP:Human @SQ SN:GL000222.1 LN:186861 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:6fe9abac455169f50470f5a6b01d0f59 SP:Human @SQ SN:GL000200.1 LN:187035 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Human @SQ SN:GL000193.1 LN:189789 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Human @SQ SN:GL000194.1 LN:191469 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Human @SQ SN:GL000225.1 LN:211173 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:63945c3e6962f28ffd469719a747e73c SP:Human @SQ SN:GL000192.1 LN:547496 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Human @SQ SN:NC_007605 LN:171823 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Human @SQ SN:hs37d5 LN:35477943 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1 SP:Human @RG ID:23726_7#16 PL:ILLUMINA PU:170912_HS36_23726_B_CB8FBANXX_7#16 LB:19474071 DS:EGAS00001001856: R&D project to develop low input library construction methods. DT:2017-09-12T01:00:00+0100 PG:SCS SM:EGAN00001575677 CN:SC @PG ID:SCS PN:RTA VN:1.18.66.3 DS:Controlling software on instrument @PG ID:basecalling PN:RTA PP:SCS VN:1.18.66.3 DS:Basecalling Package @PG ID:bambi PN:bambi PP:basecalling VN:0.9.11 DS:Convert Illumina BCL to BAM or SAM file CL:/software/solexa/pkg/bambi/0.9.11/bin/bambi i2b --intensity-dir=/nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities --basecalls-dir=/nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities/BaseCalls --lane=7 --platform-unit=170912_HS36_23726_B_CB8FBANXX_7 --read-group-id=23726_7 --study-name="EGAS00001001856: R&D project to develop low input library construction methods." --sample-alias=EGAN00001575664,EGAN00001575665,EGAN00001575666,EGAN00001575667,EGAN00001575668,EGAN00001575669,EGAN00001575672,EGAN00001575674,EGAN00001575673,EGAN00001575648,EGAN00001575649,EGAN00001575651,EGAN00001575652,EGAN00001575675,EGAN00001575676,EGAN00001575677,EGAN00001575678,EGAN00001575679,EGAN00001575680,EGAN00001575681,EGAN00001575682,EGAN00001575683,EGAN00001575684,EGAN00001575685,EGAN00001575687,EGAN00001575689,EGAN00001575690,EGAN00001575691,EGAN00001575692,EGAN00001575693,EGAN00001575695,EGAN00001575697,EGAN00001575698,EGAN00001575699,EGAN00001575701,EGAN00001575703,EGAN00001575706,EGAN00001575705,EGAN00001575707,EGAN00001575708,EGAN00001575709,EGAN00001575710,EGAN00001575711,EGAN00001575714,4254STDY7047314,EGAN00001575722,EGAN00001575720,EGAN00001575723,EGAN00001575721,EGAN00001575725,EGAN00001575726,EGAN00001575724,EGAN00001575727,EGAN00001575728,EGAN00001575729,EGAN00001575731,EGAN00001575732,EGAN00001575733,EGAN00001575734,EGAN00001575736,EGAN00001575737,EGAN00001575738,EGAN00001575739,EGAN00001575742,EGAN00001575743,EGAN00001575744,EGAN00001575746,EGAN00001575747,EGAN00001575748,EGAN00001575749,EGAN00001575750,EGAN00001575751 --output-file=- --compression-level=0 @PG ID:bamadapterfind PN:bamadapterfind PP:bambi VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamadapterfind level=0 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.9.11 CL:/software/solexa/pkg/bambi/0.9.11/bin/bambi decode --metrics-file /nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities/BAM_basecalls_20170919-115748/23726_7.bam.tag_decode.metrics --barcode-file /nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities/BAM_basecalls_20170919-115748/metadata_cache_23726/lane_7.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 PP:bambi.1 VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamcollate2 collate=2 level=0 @PG ID:bwa PN:bwa PP:bamcollate2 VN:0.7.16a-r1181 CL:/software/solexa/pkg/bwa/0.7.16a/bwa sampe /lustre/scratch117/core/sciops_repository/references/PhiX/Sanger-SNPs/all/bwa0_6/phix_unsnipped_short_no_N.fa /tmp/rHT4BtPNZv/alnphix_bwa_aln_1_out /tmp/4tjg8lafrJ/alnphix_bwa_aln_2_out /tmp/BY7PQCx5Qj/alnphix_simple_cat1_out /tmp/cIA6hK1zjr/alnphix_simple_cat2_out @PG ID:scramble PN:scramble PP:bwa VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -t 2 -I sam -O bam @PG ID:bam12auxmerge PN:bam12auxmerge PP:scramble VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/BHAO2OKXpn/simple_cat_out @PG ID:scramble.1 PN:scramble PP:bam12auxmerge VN:1.14.9 CL:/software/solexa/pkg/scramble/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:/software/solexa/pkg/scramble/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:v10.28-dirty CL:/software/solexa/pkg/pb_calibration/10.28/bin/spatial_filter -c -F /dev/stdout -t /nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities/BAM_basecalls_20170919-115748/no_cal/archive/qc/tileviz/23726_7 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 /dev/stdin ; /software/solexa/pkg/pb_calibration/10.28/bin/spatial_filter -a -f -u -l /nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities/BAM_basecalls_20170919-115748/no_cal/23726_7.bam.filter.stats -F /tmp/vGNP1dto_M/tee_post_filter_creation:__APPLY_FILTER_OUT___out /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.5 CL:/software/solexa/pkg/samtools/1.5/bin/samtools split -f /nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities/BAM_basecalls_20170919-115748/no_cal/lane7/%!.bam - @PG ID:bamcollate2' PN:bamcollate2 PP:samtools VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamcollate2 collate=1 level=0 @PG ID:bamreset PN:bamreset PP:bamcollate2' VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamreset resetaux=0 level=0 verbose=0 @PG ID:bamadapterclip PN:bamadapterclip PP:bamreset VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamadapterclip verbose=0 level=0 @PG ID:bwa' PN:bwa PP:bamadapterclip VN:0.7.16a-r1181 CL:/software/solexa/pkg/bwa/0.7.16a/bwa mem -t 8 -p -Y -K 100000000 /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/aUnH_P0xSx/alntgt_bamtofastq_out @PG ID:scramble' PN:scramble PP:bwa' VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -I sam -O bam @PG ID:samtools' PN:samtools PP:scramble' VN:1.5 CL:/software/solexa/pkg/samtools/1.5/bin/samtools reheader /tmp/AnISOZD06l/postalntgt_alterSQ_headerSQfix_out /tmp/3bOVzGqurf/postalntgt_mbuffer_headerSQfix_out @PG ID:bam12split PN:bam12split PP:samtools' VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bam12split verbose=0 level=0 @PG ID:bamsormadup PN:bamsormadup PP:bam12split VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamsormadup threads=8 SO=queryname level=0 @PG ID:bam12auxmerge' PN:bam12auxmerge PP:bamsormadup VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/PKKzyaEMU7/amp_bamadapterclip_pre_auxmerge_out @PG ID:AlignmentFilter PN:AlignmentFilter PP:bam12auxmerge' DS:Give a list of SAM/BAM files with the same set of records and in the same order but aligned with different references, split reads into different files according to alignments. You have option to put unaligned reads into one of output files or a separate file VN:V1.19 CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[./initial_phix_aln_23726_7#16.bam, /tmp/adopnhw_7t/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/3HkdqmVUmN/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=23726_7#16.bam_alignment_filter_metrics.json VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:bamsormadup' PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamsormadup threads=8 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities/BAM_basecalls_20170919-115748/no_cal/archive/lane7/bsfopt_23726_7#16.tmp PP:AlignmentFilter VN:2.0.76 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities/BAM_basecalls_20170919-115748/no_cal/archive/lane7/bmdfopt_23726_7#16.tmp M=/nfs/sf52/ILorHSany_sf52/analysis/170912_HS36_23726_B_CB8FBANXX/Data/Intensities/BAM_basecalls_20170919-115748/no_cal/archive/lane7/23726_7#16.markdups_metrics.txt PP:bamsormadup' VN:2.0.76 @PG ID:scramble.3 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -t 3 -7 -I bam -O cram -r /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @CO TY:checksum ST:all PA:all HA:crc32prod CO:2023116 BS:1327f959 NS:22512ab1 SQ:256e18aa ST:BC,FI,QT,RT,TC:38d0885a @CO TY:checksum ST:all PA:pass HA:crc32prod CO:2022800 BS:55bb61d1 NS:52a97b4 SQ:3aca34bf ST:BC,FI,QT,RT,TC:49adde3c @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:23726_7#16 PA:all HA:crc32prod CO:2023116 BS:1327f959 NS:22512ab1 SQ:256e18aa ST:BC,FI,QT,RT,TC:38d0885a @CO TY:checksum ST:23726_7#16 PA:pass HA:crc32prod CO:2022800 BS:55bb61d1 NS:52a97b4 SQ:3aca34bf ST:BC,FI,QT,RT,TC:49adde3c