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10x Genomics
Genome & Exome

Long Ranger , printed on 06/07/2025

PHASER_SVCALLER_CSPHASER_SVCALLERATTACH_PHASINGLOUPE_PREPROCESSPHASER_SVCALLER_PREFLIGHTPHASER_SVCALLER_PREFLIGHT_LOCALPHASE_STRUCTVARSSUMMARIZE_REPORTS_LINKED_READS_ALIGNERBARCODE_AWARE_ALIGNERMARK_DUPLICATESMERGE_BC_BUCKETSSETUP_CHUNKSTRIM_READS_SORT_FASTQ_BY_BARCODEBUCKET_FASTQ_BY_BCSORT_FASTQ_BY_BC_REPORTERDETECT_MOLECULESFILTER_BARCODESREPORT_BASICREPORT_COVERAGEREPORT_LENGTH_MASSREPORT_SINGLE_PARTITION_SNPINDEL_PHASERANALYZE_SNPINDEL_CALLSBARCODE_AWARE_FILTER_SNPINDELSPHASE_SNPINDELSSORT_GROUND_TRUTH_SNPINDEL_CALLERCALL_SNPINDELSCANONICALIZE_SNPINDELSFILTER_SNPINDELSPOPULATE_INFO_FIELDSSORT_SNPINDELS_STRUCTVAR_CALLERANALYZE_KNOWN_BREAKSANALYZE_SV_CALLSCALL_STRUCTVARSCOUNT_READS_BCSDETECT_OVERLAPSGET_DEPTH_INFOGET_READPAIR_EVIDENCEMERGE_SV_CALLS
←  PHASER_SVCALLER_CS

This is the main Long Ranger pipeline that performs alignment, variant calling, phasing, and structural variant calling. This outer wrapper pipeline prepares files for final output.