This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Method To Identify Viral Integration Site In Human Genome From Ngs Data?

Hi all,

Conceptually I can imagine how to do this. But, does anyone have a recommendation for a well established pipeline or tool for identifying a viral integration site in the human genome. Suppose I have 50X WGS data for a tumor sample and 30X WGS data for a normal sample and am looking for a specific virus (e.g. HBV) which is known to integrate into the genome for my cancer of interest. I want to be able to answer two simple questions: (1) Is there evidence of viral integration? (2) What is the exact breakpoint/integration site?

Any suggestions will be greatly appreciated.

genome
• 9,873 views • link
updated by jluebeck • jluebeck • written by Obi Griffith Obi Griffith

<bump>

Any update on this in 2017 .. what has been the experience and any new ones worth trying? Especially for viral integration detection from DNA capture based NGS data.

thanks!

• 0 views • link
written by Bioinfosm Bioinfosm

3 answers

My suggestion is to put human and the virus in one file, build index and then align reads with bwa-sw, bwa-mem, or bowtie2 --local -k2. You can trivially get your answer.

• 170 views • link
updated by Ram Ram • written by lh3 lh3

ViFi performs the analysis you're asking about and outperforms other existing methods (e.g. VERSE) in speed and sensitivity, particularly if coverage is low or the viral strain is evolved from the reference by any considerable amount.

https://www.ncbi.nlm.nih.gov/pubmed/29579309

• 1 views • link
written by jluebeck • jluebeck

Log in to answer this question.

More posts like this