Long Ranger2.1, printed on 05/28/2023
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:
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 \ --uiport=3600
Aside from the stage where SNPs and indels are called, longranger will behave identically as when the default FreeBayes variant caller is used.
|The path to the GATK JAR must be an absolute path (e.g., /home/jdoe/bin/GenomeAnalysisTK.jar, not just bin/GenomeAnalysisTK.jar).|