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Command executed:
bcftools annotate --header-lines /Data/data/raja/cfdna/nextflow1/bin/syn3_header.txt LCR_FILTERED > FILTERED_hd.vcf
**java -jar -Xmx4g /Data/data/raja/cfdna/nextflo…
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### Is your feature related to a problem?
We are trying to use wf-human-variation to find pathogenic variants in nanopore sequencing data of patients that have already had whole exome sequencing but …
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Using command `stub` blocks in Nextflow is useful when developing syntax and quickly testing pipelines. However, its use within nf-core is limited because the vast majority of nf-core modules do not h…
ewels updated
2 months ago
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Hello,
Does this tool also work on VCF files that have been annotated with SNPsift?
I'm using it with a SNPeff and SNPsift annotated VCF file. This is my command. It gives me a Maf file but als…
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### Operating System
CentOS 7
### Other Linux
_No response_
### Workflow Version
v2.3.1-g6a6daa6
### Workflow Execution
Command line (Local)
### Other workflow execution
_No response_
### EP…
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Write a script to apply the user's filter selections to an annotated VCF.
Input parameters:
- _Filters_: command-line arguments describing the user's filter selections, e.g. "filters=clinsig:patho…
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## Bug report
resume option works locally but not with azure batch. I've gone through all the troubleshooting steps and can't find the reason the cache is invalidated
### Expected behavior and…
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via @jxchong cc @arq5x
A user may find a variant that is not itself associated with disease, but is in a gene known to be associated with the disease. There is no way to store or query this info in g…
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recipe | lints
----------------------|----------------------
recipes/2pg_cartesian | ['missing_license']
recipes/advntr | ['should_be_noarch']
recipes/aenum | ['in_other_channels'…
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I get the same error when parsing a vcf annotated with dbNSFP ( by snpSift )
I ran the following
```python
reader = vcf.Reader(open("file.vcf"))
for line in reader:
print(line)
…
dridk updated
4 years ago