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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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wildtype amino acid sequence is real "WT"? #145

Closed susannasiebert closed 5 years ago

susannasiebert commented 6 years ago

@TotalMiss commented on Fri Jul 06 2018

I try to use pVAC-Seq to identify neoantigens. I noticed there is a germline variation next to somatice mutation,and only somatice mutations were used to identify neoantigens. I am not sure wildtype amino acid sequence was predicted use germline information or not?Shouldn't I use germline variation first?

@susannasiebert commented on Fri Jul 06 2018

pVACseq currently only evaluates one somatic mutation at a time and does not take into account proximal germline or somatic variants. However, we are working on a feature to support these cases, which should be released in a couple of months.

@susannasiebert commented on Fri Jul 06 2018

Please also note that this repository is deprecated and is no longer maintained. The pvacseq package has been superseded by the pvactools package and the repository has moved to https://github.com/griffithlab/pVACtools where all new feature development is happening. In order to have the most up-to-date features and bugfixes I highly recommend to uninstall the pvacseq package (pip uninstall pvacseq) and install pvactools (pip install pvactools). The pvacseq commands stay the same. I'm moving your issues to the pVACtools repository.

susannasiebert commented 5 years ago

In pVACtools 1.1.0 we added an option to provide a phased VCF of germline an somatic variants that are used to incorporate variants proximal to the somatic variant of interest. Please see https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep/proximal_vcf.html on how to create this VCF and how to use it.