## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/scratch/slrinzema/ghe_2022/metta/star/GRCh38-DMSO_1.samtools-coordinate-unsieved.bam] OUTPUT=/scratch/slrinzema/ghe_2022/metta/star/GRCh38-DMSO_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-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 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Tue Oct 11 14:00:43 CEST 2022 ## 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 983 26096594 22896281 0 882 4314786 0 0.165353 69956054 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19904408 19904408 2.0 1.688636 1346341 1346341 3.0 2.162855 236700 236700 4.0 2.48942 94911 94911 5.0 2.714304 52054 52054 6.0 2.869167 32921 32921 7.0 2.975811 22517 22517 8.0 3.04925 15943 15943 9.0 3.099823 11855 11855 10.0 3.134649 9277 9277 11.0 3.158632 7167 7167 12.0 3.175147 5838 5838 13.0 3.18652 4673 4673 14.0 3.194352 3888 3888 15.0 3.199745 3304 3304 16.0 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