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It would be nice if GZip VCF files could be used as input leveraging Bioconductor's [VariantAnnotation](https://bioconductor.org/packages/VariantAnnotation) R package. Plain-text MAF or tables are ine…
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I ran NanoCaller v3.6.0 on ONT NA24385 data using the default parameters:
`NanoCaller --bam ${bam} --ref ${reference} --cpu 15`
I also tried specifying the SNP and indel models:
`NanoCaller --ba…
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Some of this is an issue for the data, but some also needs some major clarifications in the spec.
- Is contig "" just a typo here:
```
@ seq4-head2[4.3/passed]; awk '!/^#/ {print $1,$2}' complexf…
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### Operating System
Other Linux (please specify below)
### Other Linux
Rocky Linux v8.6
### Workflow Version
v1.2.1
### CLI command run
```
/scratchc/jblab/nextflow run epi2me-l…
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### Code of Conduct
- [X] I have read and agree to the [Code of Conduct](https://github.com/vmware/terraform-provider-vcf/blob/main/CODE_OF_CONDUCT.md).
- [X] Vote on this issue by adding a 👍 [rea…
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Hello, I am facing an error when writing back to icloud, and I have not been able to find any relevant information online. Has anyone already faced the error ? I saw a relatively similar issue [here](…
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Hello,
I'm interested in using this pipeline for pooled data. However, when we designed the study, we used the sub-pooling method recommended by CRISP (variant caller). So instead of having a singu…
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SVAFotate ran into the error below when it was run with a manta vcf and option `--ci out`.
```
Gathering SV coordinates from VCF file: data/raw/in.vcf
Traceback (most recent call last):
File…
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Thanks for creating the tool!
I was trying scAllele on public 10x scRNA data and was able to get the output files (intronic_parts.bed, mi_summary.tab, read_cluster_info.tab and vcf). However, the vcf…
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```
file = "some_file.vcf"
vcf_reader = vcf.Reader(open(file, 'r'))
for record in vcf_reader:
print(record)
for record in vcf_reader:
print(record)
```
The second for loop doesn't print an…