## 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_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-DMSO_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-DMSO_1.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 10:12:01 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 1979 50567294 45264775 0 1814 10512407 0 0.207903 104105474 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 35741741 35741741 2.0 1.615247 3078890 3078890 3.0 1.993776 555295 555295 4.0 2.226665 214058 214058 5.0 2.369949 116922 116922 6.0 2.458104 73002 73002 7.0 2.512341 50421 50421 8.0 2.545711 36294 36294 9.0 2.566241 27436 27436 10.0 2.578872 21370 21370 11.0 2.586644 17178 17178 12.0 2.591425 13737 13737 13.0 2.594367 11599 11599 14.0 2.596176 9576 9576 15.0 2.59729 8154 8154 16.0 2.597975 6997 6997 17.0 2.598396 5928 5928 18.0 2.598656 5323 5323 19.0 2.598815 4662 4662 20.0 2.598914 3935 3935 21.0 2.598974 3518 3518 22.0 2.599011 3240 3240 23.0 2.599034 2879 2879 24.0 2.599048 2685 2685 25.0 2.599057 2387 2387 26.0 2.599062 2088 2088 27.0 2.599065 1962 1962 28.0 2.599067 1760 1760 29.0 2.599068 1634 1634 30.0 2.599069 1521 1521 31.0 2.59907 1371 1371 32.0 2.59907 1260 1260 33.0 2.59907 1204 1204 34.0 2.59907 1101 1101 35.0 2.59907 1042 1042 36.0 2.59907 960 960 37.0 2.59907 896 896 38.0 2.59907 856 856 39.0 2.59907 780 780 40.0 2.59907 740 740 41.0 2.59907 684 684 42.0 2.59907 639 639 43.0 2.59907 601 601 44.0 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