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tests/data/project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.header.sam
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| @HD VN:1.4 SO:coordinate | ||
| @SQ SN:chrM LN:16571 | ||
| @SQ SN:chr1 LN:249250621 | ||
| @SQ SN:chr2 LN:243199373 | ||
| @SQ SN:chr3 LN:198022430 | ||
| @SQ SN:chr4 LN:191154276 | ||
| @SQ SN:chr5 LN:180915260 | ||
| @SQ SN:chr6 LN:171115067 | ||
| @SQ SN:chr7 LN:159138663 | ||
| @SQ SN:chr8 LN:146364022 | ||
| @SQ SN:chr9 LN:141213431 | ||
| @SQ SN:chr10 LN:135534747 | ||
| @SQ SN:chr11 LN:135006516 | ||
| @SQ SN:chr12 LN:133851895 | ||
| @SQ SN:chr13 LN:115169878 | ||
| @SQ SN:chr14 LN:107349540 | ||
| @SQ SN:chr15 LN:102531392 | ||
| @SQ SN:chr16 LN:90354753 | ||
| @SQ SN:chr17 LN:81195210 | ||
| @SQ SN:chr18 LN:78077248 | ||
| @SQ SN:chr19 LN:59128983 | ||
| @SQ SN:chr20 LN:63025520 | ||
| @SQ SN:chr21 LN:48129895 | ||
| @SQ SN:chr22 LN:51304566 | ||
| @SQ SN:chrX LN:155270560 | ||
| @SQ SN:chrY LN:59373566 | ||
| @SQ SN:chr1_gl000191_random LN:106433 | ||
| @SQ SN:chr1_gl000192_random LN:547496 | ||
| @SQ SN:chr4_ctg9_hap1 LN:590426 | ||
| @SQ SN:chr4_gl000193_random LN:189789 | ||
| @SQ SN:chr4_gl000194_random LN:191469 | ||
| @SQ SN:chr6_apd_hap1 LN:4622290 | ||
| @SQ SN:chr6_cox_hap2 LN:4795371 | ||
| @SQ SN:chr6_dbb_hap3 LN:4610396 | ||
| @SQ SN:chr6_mann_hap4 LN:4683263 | ||
| @SQ SN:chr6_mcf_hap5 LN:4833398 | ||
| @SQ SN:chr6_qbl_hap6 LN:4611984 | ||
| @SQ SN:chr6_ssto_hap7 LN:4928567 | ||
| @SQ SN:chr7_gl000195_random LN:182896 | ||
| @SQ SN:chr8_gl000196_random LN:38914 | ||
| @SQ SN:chr8_gl000197_random LN:37175 | ||
| @SQ SN:chr9_gl000198_random LN:90085 | ||
| @SQ SN:chr9_gl000199_random LN:169874 | ||
| @SQ SN:chr9_gl000200_random LN:187035 | ||
| @SQ SN:chr9_gl000201_random LN:36148 | ||
| @SQ SN:chr11_gl000202_random LN:40103 | ||
| @SQ SN:chr17_ctg5_hap1 LN:1680828 | ||
| @SQ SN:chr17_gl000203_random LN:37498 | ||
| @SQ SN:chr17_gl000204_random LN:81310 | ||
| @SQ SN:chr17_gl000205_random LN:174588 | ||
| @SQ SN:chr17_gl000206_random LN:41001 | ||
| @SQ SN:chr18_gl000207_random LN:4262 | ||
| @SQ SN:chr19_gl000208_random LN:92689 | ||
| @SQ SN:chr19_gl000209_random LN:159169 | ||
| @SQ SN:chr21_gl000210_random LN:27682 | ||
| @SQ SN:chrUn_gl000211 LN:166566 | ||
| @SQ SN:chrUn_gl000212 LN:186858 | ||
| @SQ SN:chrUn_gl000213 LN:164239 | ||
| @SQ SN:chrUn_gl000214 LN:137718 | ||
| @SQ SN:chrUn_gl000215 LN:172545 | ||
| @SQ SN:chrUn_gl000216 LN:172294 | ||
| @SQ SN:chrUn_gl000217 LN:172149 | ||
| @SQ SN:chrUn_gl000218 LN:161147 | ||
| @SQ SN:chrUn_gl000219 LN:179198 | ||
| @SQ SN:chrUn_gl000220 LN:161802 | ||
| @SQ SN:chrUn_gl000221 LN:155397 | ||
| @SQ SN:chrUn_gl000222 LN:186861 | ||
| @SQ SN:chrUn_gl000223 LN:180455 | ||
| @SQ SN:chrUn_gl000224 LN:179693 | ||
| @SQ SN:chrUn_gl000225 LN:211173 | ||
| @SQ SN:chrUn_gl000226 LN:15008 | ||
| @SQ SN:chrUn_gl000227 LN:128374 | ||
| @SQ SN:chrUn_gl000228 LN:129120 | ||
| @SQ SN:chrUn_gl000229 LN:19913 | ||
| @SQ SN:chrUn_gl000230 LN:43691 | ||
| @SQ SN:chrUn_gl000231 LN:27386 | ||
| @SQ SN:chrUn_gl000232 LN:40652 | ||
| @SQ SN:chrUn_gl000233 LN:45941 | ||
| @SQ SN:chrUn_gl000234 LN:40531 | ||
| @SQ SN:chrUn_gl000235 LN:34474 | ||
| @SQ SN:chrUn_gl000236 LN:41934 | ||
| @SQ SN:chrUn_gl000237 LN:45867 | ||
| @SQ SN:chrUn_gl000238 LN:39939 | ||
| @SQ SN:chrUn_gl000239 LN:33824 | ||
| @SQ SN:chrUn_gl000240 LN:41933 | ||
| @SQ SN:chrUn_gl000241 LN:42152 | ||
| @SQ SN:chrUn_gl000242 LN:43523 | ||
| @SQ SN:chrUn_gl000243 LN:43341 | ||
| @SQ SN:chrUn_gl000244 LN:39929 | ||
| @SQ SN:chrUn_gl000245 LN:36651 | ||
| @SQ SN:chrUn_gl000246 LN:38154 | ||
| @SQ SN:chrUn_gl000247 LN:36422 | ||
| @SQ SN:chrUn_gl000248 LN:39786 | ||
| @SQ SN:chrUn_gl000249 LN:38502 | ||
| @RG ID:1 PL:Illumina PU:H7AP8ADXX_TAAGGCGA_1_NA12878 LB:library DS:SampleProject:NIST SM:NIST7035 CN:illuminafacility | ||
| @PG ID:bwa PN:bwa VN:0.7.5a-r405 | ||
| @PG ID:MarkDuplicates PN:MarkDuplicates CL:net.sf.picard.sam.MarkDuplicates INPUT=[/misc/ClinicalGenomicsPipeline/dev/projects/CLINICAL_NIST/work_dirs/2013_1211_162011/run/phase1_phase1_list/project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.bam] OUTPUT=/misc/ClinicalGenomicsPipeline/dev/projects/CLINICAL_NIST/work_dirs/2013_1211_162011/run/phase1_phase1_list/project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.bam METRICS_FILE=/misc/ClinicalGenomicsPipeline/dev/projects/CLINICAL_NIST/work_dirs/2013_1211_162011/run/phase1_phase1_list/project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.metrics TMP_DIR=[/misc/ClinicalGenomicsPipeline/dev/projects/CLINICAL_NIST/work_dirs/2013_1211_162011/run/phase1_phase1_list/.queue/tmp] VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates REMOVE_DUPLICATES=false ASSUME_SORTED=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false |