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Hi, after reading the docs I am still a bit confused about exactly how to generate the vcf dataframe as the input into run_UNMASC. The column names for this dataframe mentioned in the docs include:
…
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trying to downsample and test circRNA + variants on a single transcript (the one that shows up after 3 hours)
did downsampling first
```
moPepGen-util downsampleReference \
--tx-list ENST000…
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Currently using the `ensemblorg/ensembl-vep:release_95.3` image pulled from DockerHub, and experiencing 2 different issues that I don't fully understand when attempting to annotate against VCF files w…
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Hi all, I noticed that for some variants HVAR values outputted by VEP (through `--everything`) and dbNSFP v4.1a are different, as example for a file annotated thorugh VEP v103 docker, with command:
`…
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- [x] The LD table `gs://genetics-portal-data/v2d/200123/ld.parquet` now contains (i) some additional fields; (ii) variants with R2 >= 0.5 (previously R2 >= 0.7). These changes are needed for the L2G …
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Hello there!
I want to add mobile element detection using retroseq (https://github.com/tk2/RetroSeq). Retroseq produces a vcf file, and is run in two steps, discovery, and calling:
1:discovery
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Likely cause: a variant without CSQ annotations (removed with the default decision tree) in combination with genmod running in --vep mode:
```
step 4/5 inheritance matching ...
[2021-02-09 11:48:…
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Hi, while running pVACseq, the following error occurred.
* pvactools version: docker image pVACtools:2.0.4
* Operating System: ubuntu 20.04
**Describe the bug**
The error occurred in the `add_…
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Hi,
From my point of view, somatic and germline mutation should be taken together to infer changes in every transcript, and I do think this should be the best way to annotate somatic variants. Howe…
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Right now it appears that the Downstream plugin doesn't output a predicted downstream sequence for `stop_lost` variants (or it is just a sequence of multiple `X`s). Is this the expected behavior? Woul…