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I'm hitting this repeatedly when trying to load VCFs that have been merged via `bcftools merge` then normalized and decomposed via `vt` and then annotated via `vcfanno`. Note that each of these had b…
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Hi Sigve,
I'm curious if you have any hints towards producing the combined `TAL` field for a variant site that has been called by mutliple tools for a sample - just like your example VCF file:
…
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Hi, I'm working on a project to extract features from PAAD patients from the ICGC database for neoantigen immunogenicity prediction in ML. This project follows the steps taken by the model creators. I…
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Hi,
I'm trying to run SigProfilerClusters on a set of VCF files. I've successfully run SigProfilerSimulator on these files with 100 simulations, and the log file is pasted below:
-------Python a…
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Hello,
following the installation instructions for PCGR 2.0.0 via conda, I am encountering an issue when installing pcgrr. This is the exact command I am using:
```
#install PCGR
PCGR_VERSION=…
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I get an error at the short_variants:get_somatic_vcfs:smurf, seems like some vcf, row or other object being passed into smurf is empty or otherwise not assigned properly. Is there something more speci…
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Hello!
If I understand correctly, here it is about specifically somatic VCFs from `strelka2`, but not about germline:
https://github.com/griffithlab/pVACtools/blob/9642052ba082641ed2d2fd43bbcbdbe1…
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A user found an issue when running --genotype-germline-sites with Mutect2 and found that the clustered events and haplotype filters were causing false negative results.
This request was created from…
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https://ncbiinsights.ncbi.nlm.nih.gov/2023/05/04/remap-tool-to-retire/
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Hi, I hope I'm not missing anything, but in the paper that came out earlier this year, it was mentioned that there were two steps to extracting the COSMIC signatures- SigProfilerExtractor and SigProfi…