freebayes installation problems(*****)

[AnushaC]

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

[GenoMax]

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).