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10x Genomics
Chromium Genome & Exome

Understanding Output

The Long Ranger software strives to maintain compatibility with common analysis tools by using standard output file formats whenever possible. For example, the barcoded BAM files can be viewed in standard genome browsers such as IGV to verify alignment quality and other features. The Chromium-specific data, including barcodes and haplotyping, can be accessed via any third-party tools or scripts that can parse the additional elements utilized by Long Ranger.

All pipelines produce all of their output in a single pipeline output directory which, by default, is named according to the flowcell serial number for longranger mkfastq (e.g., HAWT7ADXX) and --id name for longranger wgs. Output files will appear in the outs/ subdirectory within this pipeline output directory. For example, a typical Targeted Mode run might look like:

$ cd /home/jdoe/runs
$ longranger targeted --id=sample345 \
                 --sex=female \
                 --vcmode=gatk:/path/to/gatk.jar \
                 --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \
                 --reference=/opt/refdata-hg19-2.1.0 \
                 --indices=SI-GA-A1 \
                 --targets=/home/jdoe/runs/agilent_exome.bed
 
Martian Runtime - 2.2.2
 
Running preflight checks (please wait)...
2016-05-01 12:00:00 [runtime] (ready)           ID.sample345.PHASER_SVCALLER_CS.PHASER_SVCALLER._ALIGNER.SETUP_CHUNKS
...
2016-05-02 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.bam.bai
- VCF phased:                /home/jdoe/runs/sample345/outs/phased_variants.vcf.gz
- VCF index:                 /home/jdoe/runs/sample345/outs/phased_variants.vcf.gz.tbi
- Large-scale SV calls:      /home/jdoe/runs/sample345/outs/large_sv_calls.bedpe
- Large-scale SV candidates: /home/jdoe/runs/sample345/outs/large_sv_candidates.bedpe
- Large-scale SVs:           /home/jdoe/runs/sample345/outs/large_svs.vcf.gz
- Large-scale SVs index:     /home/jdoe/runs/sample345/outs/large_svs.vcf.gz.tbi
- Mid-scale deletions:       /home/jdoe/runs/sample345/outs/dels.vcf.gz
- Mid-scale deletions index: /home/jdoe/runs/sample345/outs/dels.vcf.gz.tbi
- Loupe file:                /home/jdoe/runs/sample345/outs/loupe.loupe
 
Pipestance completed successfully!

In this case,

The contents of this outs/ directory contain the data that is described in the remainder of this section: barcoded and phased BAMs, VCFs, and SV VCFs and BEDPEs.

More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.