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Hi there,
Thanks for creating this wonderful package.
I've read your recent biorxiv paper on HGSOC ("Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational proc…
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Hi, would it be a possibility to add the EXON and INTRON fields generated by VEP to the output of the loading pipeline? We'd like to add these fields in our institute's version of Seqr (It's a highly …
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Elementary OS 5.0
VEP script 97
MySQL 5.7.27
Trying to annotate a simple test data set:
`sudo docker run -t -i -v $HOME/vep_data:/opt/vep/.vep ensemblorg/ensembl-vep`
`./vep --cache --merged …
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Hello there,
I hope you are having a great day! Thank you again for creating and maintaining this awesome pipeline. It has been extremely useful for a project I have involving A-I editing.
I j…
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#### What data file(s) does this issue pertain to?
```
snv-consensus-plus-hotspots.maf.tsv.gz
```
Potentially also CNV files. TBD.
#### What release are you using?
v12
#### Put your…
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Hi. @davidwedge @jcesar101 @sdentro
I have recently tested Battenberg on a paired sample, and it has taken approximately 14 hours. The log indicated that it was stuck at "Multi pos start: [1] "mi…
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Dear Fraternali Lab team,
I hope you are doing well.
I am currently working with your package to analyse the class-switch of a sample from which we have single-cell RNAseq and VDJ sequencing dat…
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Hi,
I am having trouble setting up my samplesheet, I keep getting errors and am confused what exactly I need to put under each column. Is "sampleset" the name of the genetic data file? You refer to i…
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Hi,
Thank you for sharing this tool with the community. After reading the manual and issues, I would like to use LongPhase for my genome projects.
FYI,
Input data: PacBio (Sequel) with ~200X c…
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Hi,
I got several questions about understanding the results when using variant_scoring.py from https://github.com/kundajelab/variant-scorer.
The main question arises from the logfc.mean, which is…