Comments (9)
Putting this on hold indefinitely since this tool takes forever to run.
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Vardict
is supposed to be parallelized within-sample by specifying to each instance a subset of genomic regions. Each vardict
instance is assigned just one core. Also, the vardict-java
implemention should be used, which also is the best supported version. See bcbio-nextgen
for a scalable implementation in Python. We are using vardict-java
in production and it is superior to the competition in many ways, especially on cancer exomes and panels. Also, it supports calling variations directly from RNA-Seq data, which may have relevance for your tool as well (if I'm not mistaken, Openvax Epidisco
uses RNA-Seq variants to see if somatic neo-epitopes are actually expressed in the tumor as an additional step in filtering).
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Interesting, thanks for the tip. I'll revisit this at the earliest.
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Great. Since you're CWL-based, as is bcbio-nextgen
, there even may be opportunities for you to integrate its scalable vardict
functionality including the optional panel and RNA-Seq modes, (or vice-versa allowing protect
integration in bcbio
) with limited effort.
We'd certainly be interested in having neo-antigen calling in bcbio
, and so may be others, right @mjafin?
from protect.
Absolutely, and thanks for clarifying VarDict best practice use Sven-Eric.
As an aside how does this tool differentiate from the likes of NetMHC and MHCFlurry?
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Hi @mjafin. Thanks for your interest in ProTECT.
ProTECT is a fully automated workflow to predict neoantigens from input Fastqs, or a combinations of vcfs, bams, haplotypes, etc. It uses the IEDB suite of tools (that encompasses NetMHC) during the pMHC prediction step.
It differs from NetMHC/MHCFlurry in that those tools are pMHC prediction tools that accept a haplotype and peptides, and provide an estimation of binding energy for each combination. ProTECT accepts sequencing data from the patient and tries to provide a immunologically relevant ranked list of neoepitopes in the patient that can guide an ACT or peptide vaccine therapy.
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Thanks for the detailed explanation @arkal .
Is there any chance you could support MHCflurry (or any other open source tool) in addition to NetMHC?
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I'd be interested in this as well since MHCflurry seemed to perform well in recent validations, and is free for commercial use afaik.
The Hammer Lab (authors of MHCflurry) also have their own neo-antigen pipeline, epidisco, so they generally know what they are doing.
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I thought i already had a ticket for that. Yes, I do want to allow and option for MHC Flurry (now #249) and I also want to look into Deep MHC (#247) as well since the Preprint shows promise.
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Related Issues (20)
- Ensure resource requirements are provided for EACH job
- Better support for ProTECT-your-way
- Update flowchart
- Update toil in make prepare to 3.8.0
- Make section in manual on contributions
- Allow mix and match of mutation callers
- Fix setuptools issue
- Allow choice of pMHC predictors
- Add github compatible license
- Transfer license to UCSC CGL
- Add troubleshooting section to the manual
- Make saving logs (if possible) a univ_option
- Add memory requirements for DNA alignment DAG
- Transgene does not export fusions
- Do not fail if >1 IARS and not all have no normal seq
- Allow user to specify majority
- providing fusion.bedpe is not compatible with snv calling HOT 1
- numerically sort positions in vcfs HOT 2
- Error when using Dockerized PHLAT
- Problem running Dockerized protect / where to find SSE-C key for downloading reference data? HOT 4
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