## 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_no_replicates/star/GRCh38.p13-D19_supernatant_DMSO_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D19_supernatant_DMSO_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D19_supernatant_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: Fri Oct 06 02:29:04 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 375 22523052 15849088 0 255 2923762 0 0.129817 79070155 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18015509 18015509 2.0 1.752128 1297593 1297593 3.0 2.317824 152310 152310 4.0 2.7433 46166 46166 5.0 3.063312 23174 23174 6.0 3.304003 14083 14083 7.0 3.485032 9452 9452 8.0 3.62119 6583 6583 9.0 3.723598 4903 4903 10.0 3.800621 3839 3839 11.0 3.858553 2966 2966 12.0 3.902125 2441 2441 13.0 3.934897 2003 2003 14.0 3.959546 1669 1669 15.0 3.978085 1310 1310 16.0 3.992028 1169 1169 17.0 4.002515 1003 1003 18.0 4.010403 877 877 19.0 4.016336 803 803 20.0 4.020798 718 718 21.0 4.024154 615 615 22.0 4.026678 575 575 23.0 4.028577 525 525 24.0 4.030005 411 411 25.0 4.031079 436 436 26.0 4.031887 384 384 27.0 4.032494 343 343 28.0 4.032951 371 371 29.0 4.033295 281 281 30.0 4.033553 277 277 31.0 4.033748 282 282 32.0 4.033894 248 248 33.0 4.034004 220 220 34.0 4.034087 205 205 35.0 4.034149 209 209 36.0 4.034196 210 210 37.0 4.034231 155 155 38.0 4.034257 171 171 39.0 4.034277 154 154 40.0 4.034292 149 149 41.0 4.034304 135 135 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