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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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View details in Rollbar: [https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5326](https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5326)
```
Traceback (most recent call last):
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**We have MAF data that is failing annotation with genome nexus (see example.csv). We are wondering why it is failing?**
- Please see an example input: [example.csv](https://github.com/genome-nexu…
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Hi, I've come across the problem that oc does not annotate SV vcf's are there plans to support SV in a future or maybe thereis a workaround?
the common line format:
`chr1 964964 20 N 137.6 . SVTYP…
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## Problem
When spec'ing boolean properties, the plugin isn't resulting the artwork expected:
1. When the selected variant doesn't include layer(s) associated with the boolean property, the artw…
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Hello,
I was trying to hard-filter the vcf files outputed by GATK HaplotypeCaller, and I want to keep variants that meet the following condition: depth (QD) < 2.0 || FisherStrand (FS) > 60.0 || root …
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**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
Our local geneticists are loo…
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Hi!
Are the variant-gene annotation files in version hg19 or version hg38?
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I've found the bug while using the `genome-nexus-annotation-pipeline`. I've noticed that `dbSNP_RS` column of maf file were not populated consistently. Sometimes I would get this column blank, while m…
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Add the annotation of called variants with SNPEff.
This will require either the creation of a local SNPEff database, or the use of reference sequences that are already included.