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10x Genomics
Genome & Exome

PHASER_SVCALLER_CSPHASER_SVCALLERATTACH_PHASINGLOUPE_PREPROCESSPHASER_SVCALLER_PREFLIGHTPHASER_SVCALLER_PREFLIGHT_LOCALSUMMARIZE_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_CALLSPHASE_SNPINDELSSORT_GROUND_TRUTH_SNPINDEL_CALLERCALL_SNPINDELSCANONICALIZE_SNPINDELSFILTER_SNPINDELSPOPULATE_INFO_FIELDSSORT_SNPINDELS_STRUCTVAR_CALLERANALYZE_SV_CALLSCALL_STRUCTVARSCOUNT_READS_BCSDETECT_OVERLAPSFILTER_PILEUPSGET_HAP_COVERAGEGET_LOW_DEPTH_LOCIGET_READPAIR_EVIDENCEGET_READPAIR_LOCIMERGE_SV_CALLSPREPARE_SVCALLING_RANGES
  PHASER_SVCALLER_CS

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