We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

KNOWNSITES

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.

Comments

  • 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

Sign In or Register to comment.