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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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