## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-DMSO_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-DMSO_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-DMSO_3.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/tmp] MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false 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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Wed Oct 04 10:55:52 CEST 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 Unknown Library 966 24161375 16264721 0 858 3891097 0 0.161061 66723016 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18673618 18673618 2.0 1.696203 1153570 1153570 3.0 2.180901 196845 196845 4.0 2.518349 79673 79673 5.0 2.753281 43495 43495 6.0 2.916841 26903 26903 7.0 3.030713 18136 18136 8.0 3.10999 13314 13314 9.0 3.165183 9652 9652 10.0 3.203609 7491 7491 11.0 3.230361 5835 5835 12.0 3.248986 4664 4664 13.0 3.261952 3963 3963 14.0 3.27098 3173 3173 15.0 3.277265 2678 2678 16.0 3.28164 2411 2411 17.0 3.284686 2033 2033 18.0 3.286807 1687 1687 19.0 3.288284 1508 1508 20.0 3.289312 1361 1361 21.0 3.290027 1204 1204 22.0 3.290526 1042 1042 23.0 3.290873 919 919 24.0 3.291114 865 865 25.0 3.291282 775 775 26.0 3.291399 708 708 27.0 3.291481 590 590 28.0 3.291538 614 614 29.0 3.291577 576 576 30.0 3.291605 528 528 31.0 3.291624 457 457 32.0 3.291637 418 418 33.0 3.291646 376 376 34.0 3.291653 381 381 35.0 3.291657 342 342 36.0 3.29166 324 324 37.0 3.291663 309 309 38.0 3.291664 280 280 39.0 3.291665 258 258 40.0 3.291666 248 248 41.0 3.291666 253 253 42.0 3.291667 219 219 43.0 3.291667 201 201 44.0 3.291667 240 240 45.0 3.291667 173 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