## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2012-08-25/US_Cal_Pla_1_2012-08-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2012-08-25/US_Cal_Pla_1_2012-08-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2012-08-25/US_Cal_Pla_1_2012-08-25.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: Fri Jan 20 19:36:53 UTC 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 lib1 9261510 71237713 0 0 4856657 4775875 0 0.094956 507275379 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 61022436 61022436 2.0 1.868983 3736135 3736135 3.0 2.624114 221422 221422 4.0 3.280309 20145 20145 5.0 3.850532 5082 5082 6.0 4.346046 2532 2532 7.0 4.776639 1528 1528 8.0 5.150817 980 980 9.0 5.475971 679 679 10.0 5.758524 521 521 11.0 6.004058 353 353 12.0 6.217423 271 271 13.0 6.402833 226 226 14.0 6.563951 201 201 15.0 6.70396 167 167 16.0 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