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Hello everyone!
In a fresh 1.2.0 bcbio installation variant calling with `hlacaller: optitype` fails at
https://github.com/FRED-2/OptiType/blob/master/OptiTypePipeline.py#L231
A fresh one has…
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Hi there,
I am trying to run OptiType, but it crashes after loading the reads:
`128K...129K...130K...
0:05:47.06 130124 reads loaded. Creating dataframe...
Traceback (most recent call last):
…
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Hello.
Today I got this error:
```
Traceback (most recent call last):
File "/soft/OptiType-1.3.2/OptiTypePipeline.py", line 433, in
hlatype = result.iloc[0][["A1", "A2", "B1", "B2", "C1"…
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Hello OptiType developers!
Thanks for developing and supporting OptiType!
In a fresh 1.2.0 bcbio installation variant calling with `hlacaller: optitype` fails at
https://github.com/FRED-2/Opt…
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**Background**
Create **OptiType** tool class that includes working logic of this tool in Fonda. Tool class should implement Tool interface.
**Approach**
- find all tool usage in Fonda workfl…
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When I run the command `nextflow run nf-core/hlatyping --reads '*_R{1,2}.fastq.gz' -profile docker`, it fails in the `pre_map_hla`step with the following error:
```
Command error:
Open failed …
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hisatgenotype --base genotype_genome -p 20 -1 HLA_H9-0193QC_S1_R1_001.fastq -2 HLA_H9-0193QC_S1_R2_001.fastq
1: Extracting reads from HLA_H9-0193QC_S1_R1_001.fastq
No genotype_genome_backbon…
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I've traced the error to vt normalize in this line of ggd-run.sh:
```
bcftools view -f PASS $vcf_file | bcftools annotate -x "^$fields_to_keep" -Ov | vt decompose -s - | vt normalize -r $ref -n - …
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Hi!
when running variant calling on hg38 with disambiguate on mm10:
```
details:
- algorithm:
aligner: bwa
coverage: /path/coverage.bed
coverage_interval: regional
disambig…
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Hi, I have installed HLAtyping with nextflow, I can run
`nextflow run nf-core/hlatyping -profile docker,test --outdir $PWD/results
`
However, I want to use my own bam file as input, so I used thi…