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### Snakemake pipeline steps
**Alignment and quality control**
- [x] align
- [x] fingerprint
- [x] gencode
**Somatic variant calling**
- [x] mutect
- [x] m2db
**Copy number calling**
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I'm so glad to find your great software NEOPREDPIPE to predict tumor neoantigens easliy. However, I got an error when running the NeoPredPipe,the bug shows as following .I have checked my reformat fas…
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https://mp.weixin.qq.com/s/B1l_-1nsnVmW-uHoqD7Dow
ixxmu updated
2 years ago
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https://mp.weixin.qq.com/s/3oJll69icjMRumczUYlJLA
ixxmu updated
2 years ago
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https://mp.weixin.qq.com/s/OzE6J9DxebsWcmiuvq8fBQ
ixxmu updated
2 years ago
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https://mp.weixin.qq.com/s/3oJll69icjMRumczUYlJLA
ixxmu updated
2 years ago
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Your Wildtype and Frameshift plug-ins are very useful. Have you considered also making a plug-in for mutations on splice site regions?
Thanks
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MOAlmanac is a cancer variant knowledgebase from BROAD/Dana-Farber with 820 assertions.
The API documentation is here: https://app.swaggerhub.com/apis-docs/vanallenlab/almanac-browser/0.2#/
Con…
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Hello,
I am using docker to run antigen.garnish and I think everything worked as intended so far.
However, when I run
```R
# predict neoantigens
result % garnish_affinity(.)
```
I get the fol…
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Hello,
i am running the pvacseq command with the `-p` option. The phased vcf file I created according to [this](https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep/proximal_vcf.html). …