Question: NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
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gravatar for Ash
6 weeks ago by
Ash10
Ash10 wrote:

I have called variants with GRCm38 and annotated with snpeff with in built GRCm38.99.genome. When doing snpefftomaf.pl NCBI build column in the MAF file is 37?

I checked the header of the VCF and confirmed it was GRCm38 that I used.

Is there a way to check if the NCBI build was detected wrong or if I did use the wrong build?

Thank you again!

ADD COMMENTlink written 6 weeks ago by Ash10

What is snpefftomaf.pl, is this a custom script? Not much to say without you linking to the source of that tool.

ADD REPLYlink written 6 weeks ago by ATpoint46k

Hi, this is the tool https://github.com/tsy19900929/snpeffToMaf

ADD REPLYlink written 6 weeks ago by Ash10

It has build 37 hardcoded according to the source code, nothing you can do about it. I did not check though whether this line has any impact on the code, there is no documentation available therefore random scripts from Github are usually to be used with care. Maybe open an issue and ask the developer what to do.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by ATpoint46k
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