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  • AnushaC
    Member
    • Sep 2013
    • 78
    #1

    freebayes installation problems(*****)

    Dear All,

    I installed freebayes

    achimmiri@idash-cloud-979:/mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/CD4/freebayes$ ls
    bamtools examples Makefile paper scripts ttmath
    bin intervaltree NA12878.chr20.broad_truth_set.20131119.snps_and_indels.genotypes.vcf.gz python src vcflib
    CONTRIBUTORS LICENSE NA12878.chr20.broad_truth_set.20131119.snps_and_indels.genotypes.vcf.gz.tbi README.md test

    I installed everything properly but i still see
    achimmiri@idash-cloud-979:/mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/CD4/freebayes$ vcfroc
    vcfroc: command not found
    achimmiri@idash-cloud-9979:/mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/CD4/freebayes$ vcfroc
    vcfroc: command not found
    achimmiri@idash-cloud-979:/mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/CD4/freebayes$ vcfintersect
    vcfintersect: command not found
    achimmiri@idash-cloud-979:/mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/CD4/freebayes$ ls
    bamtools examples Make
    but when i use like this
    achimmiri@idash-cloud-979:/mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/CD4/freebayes$ freebayes vcfroc
    Please specify a fasta reference file.
    achimmiri@idash-cloud-979:/mnt/oncogxA/anusha/DGFDATA_Tissue_DATA/CD4/freebayes$ freebayes vcfintersect
    Please specify a fasta reference file.
    it is always asking for a reference file
    does any body know how to plot roc curve from your vcf file
    Thanks so much

    Anusha
    Tags: None
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    This is not a problem with installation but command-line usage.

    Every freebays command needs you to specify the reference in fasta format (-f ref.fa) (see examples on this page (https://github.com/ekg/freebayes).
    Last edited by GenoMax; 06-16-2015, 05:19 AM.

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