NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow

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3.9 years ago

whb ▴ 60

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!

MAF genome reference GRCm38 NCBI build • 1.0k views

ADD COMMENT • link 3.9 years ago by whb ▴ 60

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

ADD REPLY • link 3.9 years ago by ATpoint 85k

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

ADD REPLY • link 3.9 years ago by whb ▴ 60

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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 REPLY • link 3.9 years ago by ATpoint 85k

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