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Hi,
I have a problem about inputfile.
I have vep.vcf file that include chromosome position with "chr".
but my readcount file have not "chr" letter, DNA(normal,tumor),RNA all of them.
so, I alt…
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Hi, we have some VCF files that are all failing this for different reasons. They are all submitted by different teams, and have been generated with a variety software. I'm wondering if someone could h…
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Hi there,
I am trying to call neoepitopes using a locally installed version of topiary and NetMHCpan, and keep running into this error
> Traceback (most recent call last):
> File "/usr/loca…
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It is straightforward to filter all predicted neoepitopes against the human entire peptidome. Perhaps this is only required for 8mers or 9mers, probabilistically. It seems that `stringi` is the right …
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To enable:
1. Neoepitope predictions from gene fusions
- [JAFFA](https://github.com/Oshlack/JAFFA/): de novo assembly of raw RNA reads aligned to a reference transcriptome -> cDNA with identi…
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@jpfeil can you look at this?
arkal updated
7 years ago
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Given the name/purpose of this pipeline ("Personalized cancer **epitope discovery** and **peptide vaccine prediction** pipeline"), I think we should run topiary by default in addition to vaxrank and i…
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What needs to get done first:
- [x] [Create topiary target](https://github.com/hammerlab/biokepi/issues/37)
- [x] [Add HLA typing](https://github.com/hammerlab/biokepi/issues/33)