## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_3_2015-08-26/UA_Kie_Cho_3_2015-08-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_3_2015-08-26/UA_Kie_Cho_3_2015-08-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_3_2015-08-26/UA_Kie_Cho_3_2015-08-26.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Jan 20 16:43:46 UTC 2023 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE lib1 39624319 10688697 0 0 10738420 887818 0 0.205143 60727617 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 8912392 8912392 2.0 1.838609 536537 536537 3.0 2.541875 41155 41155 4.0 3.131639 5575 5575 5.0 3.626222 1962 1962 6.0 4.040983 1261 1261 7.0 4.388805 910 910 8.0 4.680492 638 638 9.0 4.925104 465 465 10.0 5.130238 392 392 11.0 5.302264 297 297 12.0 5.446528 241 241 13.0 5.567508 218 218 14.0 5.668964 214 214 15.0 5.754045 191 191 16.0 5.825395 147 147 17.0 5.88523 128 128 18.0 5.935408 110 110 19.0 5.977488 149 149 20.0 6.012776 124 124 21.0 6.042369 108 108 22.0 6.067186 102 102 23.0 6.087998 104 104 24.0 6.105451 106 106 25.0 6.120088 80 80 26.0 6.132362 76 76 27.0 6.142655 90 90 28.0 6.151287 59 59 29.0 6.158526 71 71 30.0 6.164596 81 81 31.0 6.169687 65 65 32.0 6.173956 54 54 33.0 6.177537 59 59 34.0 6.180539 57 57 35.0 6.183057 47 47 36.0 6.185168 47 47 37.0 6.186939 54 54 38.0 6.188424 42 42 39.0 6.189669 41 41 40.0 6.190714 33 33 41.0 6.191589 33 33 42.0 6.192324 39 39 43.0 6.19294 35 35 44.0 6.193456 25 25 45.0 6.193889 27 27 46.0 6.194252 28 28 47.0 6.194557 27 27 48.0 6.194813 28 28 49.0 6.195027 14 14 50.0 6.195206 23 23 51.0 6.195357 14 14 52.0 6.195483 16 16 53.0 6.195589 25 25 54.0 6.195678 19 19 55.0 6.195753 13 13 56.0 6.195815 19 19 57.0 6.195868 18 18 58.0 6.195912 11 11 59.0 6.195948 22 22 60.0 6.195979 12 12 61.0 6.196005 11 11 62.0 6.196027 11 11 63.0 6.196045 15 15 64.0 6.19606 11 11 65.0 6.196073 21 21 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