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Some TCGA mutations are currently duplicated. This is because Annovar aggregates effects of duplicated mutations in input and paste these together with semicolons.
To solve this issue, we need to se…
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**Description**
`subsetMaf()` behaves weird / throws error when applied on a maf object created using `annovarToMaf()`. Other functions like oncoplot, rainfallplot etc behave weird, too, probably due …
sribi updated
7 years ago
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Hi,
I am using JAnnovar to annotate a VCF file after variant calling with GATK.
The same file I used in Annovar without problems makes Jannovar complain like this:
*_### ERROR StatusLogger No log4j2…
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I haven't noticed this before and I'm trying to figure out what is happening. A recent file that I'm processing with ANNOVAR is being renamed (filename is truncated) during processing, resulting in an…
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The spec doesn't say anything about using directories as inputs/outputs. Quite a bit of tools use directories, so we'll need to support that.
A workaround that has been used is to just treat them as …
ghost updated
7 years ago
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When annotating with table_annovar.pl, my output VCF file contains several new entries in the INFO column, as expected. However these new INFO values are not added to the meta-information header lines…
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Forgive the lengthiness. I'm new.
I’ve been working with the gap annotator to include it into cpipe and have added it to the pipeline on meerkat: /misc/vcgs/exome/dev. I have noticed some interestin…
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Hi,
I've been using ANNOVAR with great results for a long time now, thank you for great work. I recently decided to switch from using the *multianno.txt output format to the more cross-compatible *mu…
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Hi,
As far as I understand, if I were to use GRCh38 reference for my VCF, the corresponding hg38 annotations would have to be downloaded and probably saved in the `/path/to/gemini/data/gemini_data/` …
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This thread is to discuss the conceptual structure and scope of variant annotation schemas.
Currently methods like VEP, SnpEff, Annovar, and Varant provide annotation in the VCF file in ways that emb…