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Hi,
I am running into an issue with the HLA typing that I cannot figure out. The program fails with the message:
Traceback (most recent call last):
File "bin/optitype_ext.py", line 31, in
…
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Hello!
Thank you for creating a great pipeline for assessing HLA imputation accuracy. I am planning to use HIBAG for imputing Sudanese genomes. Where I could obtain HLA_Type_Table for individuals o…
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As far as I understand it from your paper, BigMHC supports predictions for all human class I alleles. However, it doesn't restrict the input provided to the -a option to only human class I HLA alleles…
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### Installation Type
Docker
### pVACtools Version / Docker Image
griffithlab/pvactools:4.4.1
### Python Version
_No response_
### Operating System
_No response_
### Describe the bug
Hello! A…
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Is there any way to obtain the quality (r2 or INFO) of imputing HLA-* ?
So far, after doing the prediction I can only see the alleles and only one probability.
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I'm using optitype/1.3.1, specifying solver=cbc in config.ini, using hla_reference_dna.fasta. i prefilter my reads using razers3. This is the output i'm getting with my own data.
```
A1 …
kylec updated
4 years ago
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- **Workflow changes**
- [x] Sample name as workflow parameter for better output dataset naming
- [x] PEAR
- [x] give percentage along with count
- [x] adapter clipping (Cutadapt)
- [ ]…
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Hello, team.
First I want to say thanks to this nice tool.
Other functions in this tool work good like _genotype_. in my single cell RNA sequencing data (+single end).
I downloaded this tool f…
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When making prediction using predict.py, here is the example input
,CDR3b,CDR3a,peptide,MHC,binder
0,CASSIRASYEQYF,CAGASGNTGKLIF,GILGFVFTL,HLA-A*02:01,1
1,CASSIRSTDTQYF,CAGSGGGSQGNLIF,GILGFVFTL,H…
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Hi Christophe! Thank you for making this tool available.
I have two questions about it: Did you calculate the Grantham distance for the loci that Pierini F & Lenz TL did not analyze (or did not inclu…