Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

gene fusion feature request. #36

Open
pl618 opened this issue May 19, 2018 · 2 comments
Open

gene fusion feature request. #36

pl618 opened this issue May 19, 2018 · 2 comments

Comments

@pl618
Copy link

pl618 commented May 19, 2018

Hi, Sigven, Now PCGR can analysis SNV/INDEl and CNA. would you like to add gene fusion function in the future?

Another question is that given tumor/normal raw data(fastq), can you recommend some pipeline to generate accurate variant file(vcf) ? The vcf looks like pcgr's examples, has multiple variant caller info.
This info can display on the HTML report.

thanks !

@sigven
Copy link
Owner

sigven commented May 25, 2018

Dear Peng,
Thanks for your question, very relevant. The answer is yes, I want to have functionality for this :-) There are, as you probably are aware of, a number of biomarkers in the CIViC database that are linked to gene fusions, and which PCGR is currently not able to support. I am afraid I cannot provide any timeline as to when this can be offered, as one needs to figure out how the input should be defined, whether one should include any quality annotations pr. fusion etc. (I have little experience in this particular field, i.e. fusion detection in cancer). If you have any ideas, these are very welcome.

Regarding your other question, choice of somatic variant detection pipeline, there are a number of options available. In general, making a consensus set from multiple calling algorithms have proven to be strategy that can minimize the impact of false positive calls. In this regard, the pipelines provided by bcbio is very solid, a number of PCGR users are using these.

regards,
Sigve

@sigven sigven closed this as completed May 25, 2018
@sigven sigven reopened this May 25, 2018
@Sidra-TBI-FCO
Copy link

Maybe some inspiration can be found here: https://github.com/nf-core/rnafusion

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

3 participants