Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.


francismfrancism NigeriaMember

please, am new to GATK and presently running a yam GBS but need a known site for me to run my baserecalibration . How do generate my knowsites.


  • francismfrancism NigeriaMember

    java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R /nfs/francis/Yam/yam_num.fasta -I /nfs/francis/Yam/C5D3EACXX_6_realigned_reads.bam -o /nfs/francis/Yam/C5D3EACXX_6_recal_data.grp
    java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R /nfs/francis/Yam/yam_num.fasta -I /nfs/francis/Yam/ C6A89ANXX_1_realigned_reads.bam -o /nfs/francis/Yam/C6A89ANXX_1_recal_data.grp

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