namphuon/ViFi

ViFi For germline

Closed this issue · 3 comments

Jordi-V commented

Hi everyone,

I'have a question about ViFi, I want to detect a germline virus integrations in my samples, I want to know if its possible use ViFi for this prupose... Even more, If I have different files for fastq_1 and fastq_2 I'have to merge all of them in one for _1 and other for _2??

Thanks for your help

Jordi

Jordi-V commented

Sorry, final question is where I can found the ref genome + viruses used in your program...

Thanks

Jordi

Jordi-V commented

Sorry, I have WGS DNA samples, so I can use the VIFI? I need mRNA??

Thanks

namphuon commented

Hi Jordi,

Very sorry for long delay. I've completely overhauled all of ViFi in order to fix the many software version issues. Included with this overhaul is a new pipeline for building the reference dataset, but briefly, if you follow the new instructions and run the setup_linux_mac.sh script, it will build the hg19+hpv reference data for you.

ViFi takes both WGS and RNA-seq data.