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10x Genomics
Chromium Genome & Exome

Using GATK with Long Ranger

By default longranger uses FreeBayes to call SNPs and indels, but support is also provided for using GATK's HaplotypeCaller. Be aware of the following requirements for using GATK with Long Ranger:

  1. You must be properly licensed to use GATK. The Long Ranger software does not include a license for GATK.
  2. You must already have a working version of GATK installed on your system.
  3. You must use GATK 3.2, 3.4, 3.5 or 3.7. GATK version 3.6 has a crashing bug in the 'single-haplotype' mode which is used by Long Ranger.
  4. If you are using a custom reference, you must create a genome.dict file. See the mkref script for details.

You can instruct longranger to use GATK as it's variant caller by passing the --vcmode=gatk:/path/to/GenomeAnalysisTK.jar parameter. For example if your GenomeAnalysisTK.jar jarfile is located in /usr/local/gatk/GenomeAnalysisTK.jar,

$ longranger wgs --id=sample345 \
                 --sex=female \
                 --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \
                 --indices=SI-GA-A1 \
                 --reference=/opt/refdata-hg19-2.1.0 \
                 --targets=/home/jdoe/runs/agilent_exome.bed \
                 --vcmode=gatk:/usr/local/gatk/GenomeAnalysisTK.jar \

Aside from the stage where SNPs and indels are called, longranger will behave identically as when the default FreeBayes variant caller is used.