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Current code is expecting indels to be handled in the usual Jannovar way e.g.
1 12345 . TG 0.01
rather than
1 12345 A ATG 0.01
and
1 12344 AT .
rather than
1 12345 AAT A
…
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Hi,
For my maf file, some variants are classified as UNKNOWN by annovar. on the oncoplot, it does not have any color showing it.
Thanks,
Ming
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I am getting below error while running this command
Can you help, thanks
./Intervar.py', '-c', 'config.ini'
File "./Intervar.py", line 1631, in
main()
File "./Intervar.py", line 1601, in m…
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Hi Gemini developers and users!
Thank you for the excellent tool!
Gemini supports VEP/Snpeff annotations.
Do you have any plans to support Annovar or arguments why VEP is better?
Personally …
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Hello,
I am trying to run the PSAP pipeline using a somatic variant callset, but I'm getting an error during the PSAP annotation step. Here is the traceback:
Read 19714 items
[1] 5794 26
Rea…
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In order to integrate clinical interpretations of variants from the WC PMKB database (here: https://pmkb.weill.cornell.edu/therapies/download.xlsx , https://pmkb.weill.cornell.edu/), the provided Exce…
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We're having trouble getting the scripts to run. Do you have any example data you can provide to ensure we have everything in the proper format? Also, which version of R is required? Some specific li…
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Dear Mr. Wang,
Would it be possible to get to some kind of licensing agreement to make it possible to make ANNOVAR available as a package in de conda package manager.
Conda is being widely used thro…
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When I use speedseq var on my bam file of a whole genome, it seems going to take forever to finish. I stopped it after 43 hrs, a vcf.gz file was made and the vcf format looks decent. Below is the code…
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Hi there,
I'm looking to merge some VCF files but when I try I get the following error message.
"Incorrect number of GL fields (3) at chr1:12719, cannot merge."
Input command :
bcftools mer…
eddip updated
7 years ago