Skip to main content

Long Ranger

Sample demultiplexing, barcode processing, alignment, quality control, variant calling, phasing, and structural variant calling

https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger

Currently supported Longranger pipelines:

  • wgs
  • targeted
  • align

Usage:

longranger wgs --fastqs=/path/to/fastq --id=NA12878
multiqc /path/to/NA12878

This module will look for the files _invocation and summary.csv in the NA12878 folder, i.e. the output folder of Longranger in this example. The file summary.csv is required. If the file _invocation is not found the sample will receive a generic name in the MultiQC report (longranger#1), instead of NA12878 or whatever was given by the --id parameter.

File search patterns​

longranger/invocation:
  contents: call PHASER_SVCALLER_CS(
  fn: _invocation
  max_filesize: 2048
longranger/summary:
  contents: longranger_version,instrument_ids,gems_detected,mean_dna_per_gem,bc_on_whitelist,bc_mean_qscore,n50_linked_reads_per_molecule
  fn: "*summary.csv"
  num_lines: 2