## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//CY_Nic_14_11/CY_Nic_14_11.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/CY_Nic_14_11/CY_Nic_14_11.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/CY_Nic_14_11/CY_Nic_14_11.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: Sun Jun 07 09:54:05 UTC 2020 ## 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 5923714 31889354 0 0 1753441 942648 0 0.052204 528718189 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 29688316 29688316 2.0 1.941468 710342 710342 3.0 2.827831 13779 13779 4.0 3.662314 1121 1121 5.0 4.447953 542 542 6.0 5.187607 335 335 7.0 5.883968 281 281 8.0 6.53957 219 219 9.0 7.156799 154 154 10.0 7.7379 153 153 11.0 8.284989 143 143 12.0 8.800056 124 124 13.0 9.284974 127 127 14.0 9.74151 111 111 15.0 10.171324 89 89 16.0 10.575981 116 116 17.0 10.956952 89 89 18.0 11.315624 94 94 19.0 11.653303 83 83 20.0 11.971217 91 91 21.0 12.270523 74 74 22.0 12.55231 69 69 23.0 12.817604 60 60 24.0 13.067369 50 50 25.0 13.302515 48 48 26.0 13.523898 53 53 27.0 13.732323 43 43 28.0 13.928549 56 56 29.0 14.113289 51 51 30.0 14.287216 32 32 31.0 14.450963 33 33 32.0 14.605125 46 46 33.0 14.750264 35 35 34.0 14.886908 42 42 35.0 15.015554 32 32 36.0 15.13667 42 42 37.0 15.250697 28 28 38.0 15.35805 35 35 39.0 15.459119 20 20 40.0 15.554273 27 27 41.0 15.643857 30 30 42.0 15.728197 23 23 43.0 15.807601 19 19 44.0 15.882357 24 24 45.0 15.952738 25 25 46.0 16.018999 9 9 47.0 16.081382 23 23 48.0 16.140113 22 22 49.0 16.195407 16 16 50.0 16.247465 18 18 51.0 16.296475 15 15 52.0 16.342617 14 14 53.0 16.386058 12 12 54.0 16.426956 16 16 55.0 16.46546 18 18 56.0 16.501711 16 16 57.0 16.53584 19 19 58.0 16.567971 27 27 59.0 16.598222 12 12 60.0 16.626702 12 12 61.0 16.653515 22 22 62.0 16.678759 6 6 63.0 16.702525 12 12 64.0 16.7249 11 11 65.0 16.745965 17 17 66.0 16.765797 13 13 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