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During vcf2txt using seqtool error vcf melt, there was an error:
```
pkg_resources.DistributionNotFound: pylev
```
Details please see below
```
module load R/3.0.0; cat SUBJECT/RMS2096/RMS2096blood…
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### Description of the bug
Hi,
The pipeline is executing succesfully until the end but skip annotation processes despite params.annotate_tool is not null. I tried to set it up with 'vep' and 'merg…
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@jblachly any suggestions? I feel that our atomizer should be able to parse out information/annotations so that it is compatible with many different annotated vcfs. I assume we should be able to parse…
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When trying to load a VCF in IGV it gives the following error message:
```
The provided VCF file is malformed at approximately line number 69: The VCF specification does not allow for whitespace in th…
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I am currently comparing the IMPACT categories HIGH, MODERATE, LOW and MODIFIER of VEP, snpEff and ANNOVAR.
```
perl $ANNOVAR/table_annovar.pl ${SCRATCH}/$FILEBASENAME/$interval.vcf.gz $ANNOVAR/h…
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I have the most previous experience with SnpEff/ClinEff. Do people here have preferences as to which tool if any to run and any non-standard parameters to use?
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added AVIA_not_found column. It seems AVIA does not have complete MAF list.
Case | Khanlab | AVIA | Both | Khanlab Only | AVIA Only | AVIA Only Not Found | Khanlab Only (%) | AVIA Only (%) | AVIA O…
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Getting the following error when trying to estimate `median_vaf_purity` on a combined/merged VCF file.
```python
/home/jacquelineburos/projects/cohorts/cohorts/functions.py in grab_vaf(variant)
…
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### Description of the bug
Hi it is my first time trying to use sarek pipeline and in general nexflow and nf-core. I was to run only the annotation part with input vcf.
I am geting the following …
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Hello everyone!
bcbio1.2.9 is out - thanks everyone who contributed to testing and bug fixing during the last month!
We were lucky enough to catch openssl1.1.1 > 3.0 upgrade (Sept 2021) which is…