Long Ranger2.0, printed on 05/16/2022
Long Ranger's Whole Genome Mode analyzes sequencing data from a Chromium-prepared library. This involves the following steps:
Run longranger demux on the Illumina BCL output folder to generate FASTQ files.
Run longranger run for each sample that was demultiplexed by longranger demux.
For the following example, assume that the Illumina BCL output is in a folder named
First, follow the instructions on running longranger demux to generate FASTQ files. For example, if the flowcell serial number was
HAWT7ADXX, then longranger demux will output FASTQ files in
To run Long Ranger in whole genome mode, you use the longranger run command, with the following parameters:
|A unique run ID string: e.g. |
|Sex of the sample: |
|Path of the FASTQ folder generated by longranger demux|
|Path to a 10x compatible reference, e.g. |
See Installation for how to download and install the default reference.
|(optional) Sample indices associated with this sample. Comma-separated list of:
|(optional) Lanes associated with this sample|
|(optional) Sample name as specified in the sample sheet supplied to |
|(optional) Path to a "pre-called" VCF file. Variants in this file will be phased.|
longranger mkvcfto extract samples and standardize your VCF files. Run
longranger mkvcf --helpfor details.
After determining these input arguments, call longranger run:
$ cd /home/jdoe/runs $ longranger run --id=sample345 \ --sex=female \ --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \ --reference=/opt/refdata-hg19-2.0.0 \ --indices=SI-GA-A1 \
Following a set of preflight checks to validate input arguments, Long Ranger pipeline stages will begin to run:
longranger run 2.0.1 Copyright (c) 2016 10x Genomics, Inc. All rights reserved. ----------------------------------------------------------------------------- Martian Runtime - 2.0.1 Running preflight checks (please wait)... 2016-05-01 12:00:00 [runtime] (ready) ID.sample345.PHASER_SVCALLER_CS.PHASER_SVCALLER._ALIGNER.SETUP_CHUNKS 2016-05-01 12:00:00 [runtime] (run:local) ID.sample345.PHASER_SVCALLER_CS.PHASER_SVCALLER._SNPINDEL_PHASER.SORT_GROUND_TRUTH 2016-05-01 12:00:00 [runtime] (run:local) ID.sample345.PHASER_SVCALLER_CS.PHASER_SVCALLER._SNPINDEL_PHASER.SORT_GROUND_TRUTH.fork0.chnk0.main ...
By default, longranger run will use all of the cores available on your
system to execute pipeline stages. You can specify a different number of cores
to use with the
--localcores option; for example,
will limit the pipeline to using up to sixteen cores at once. Similarly,
--localmem will restrict the amount of memory (in GB) used by
The pipeline will create a new folder named with the sample ID you specified (e.g.
/home/jdoe/runs/sample345) for its output. If this folder already exists, Long Ranger will assume it is an existing pipestance and attempt to resume running it.
By default, longranger run calls SNPs and indels with Freebayes, phases those variants, and adds structural variant calls. GATK may also be used.
Alternatively, you may provide an existing VCF file as an input to the pipeline. In this "pre-called VCF" mode, longranger run does not call SNPs and indels itself, but phases the variants in the supplied VCF file, and also outputs structural variant calls.
As of Long Ranger 2.0, longranger run no longer supports setting the --vcmode argument when supplying a pre-called VCF file.
A successful longranger run execution should conclude with a message similar to this:
2016-05-02 15:46:41 [runtime] (run:local) ID.sample345.PHASER_SVCALLER_CS.PHASER_SVCALLER.LOUPE_PREPROCESS.fork0.join 2016-05-02 15:46:44 [runtime] (join_complete) ID.sample345.PHASER_SVCALLER_CS.PHASER_SVCALLER.LOUPE_PREPROCESS 2016-05-02 15:46:55 [runtime] VDR killed 4738 files, 223GB. Outputs: - Run summary: /home/jdoe/runs/sample345/outs/summary.csv - BAM barcoded: /home/jdoe/runs/sample345/outs/phased_possorted_bam.bam - BAM index: /home/jdoe/runs/sample345/outs/phased_possorted_bam_index.bam.bai - VCF phased: /home/jdoe/runs/sample345/outs/phased_variants.vcf.gz - VCF index: /home/jdoe/runs/sample345/outs/phased_variants_index.vcf.gz.tbi - SV calls: /home/jdoe/runs/sample345/outs/sv_calls.bedpe - SV candidates: /home/jdoe/runs/sample345/outs/sv_candidates.bedpe - Loupe file: /home/jdoe/runs/sample345/outs/loupe.loupe Pipestance completed successfully!
The output of the pipeline will be contained in a folder named with the sample ID you specified (e.g.
sample345). The subfolder named
outs will contain the main pipeline output files:
|Run summary metrics in CSV format|
|Aligned reads annotated with barcode information|
|Index for |
|VCF annotated with barcode and phasing information|
|Index for |
|Confidently called structural variants with phasing information|
|Structural variant candidates failing one or more filters|
|File that can be opened in the Loupe genome browser|