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HGLab / VIC

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Support for GRCh38 #4

Open praveenraj2018 opened 3 years ago

praveenraj2018 commented 3 years ago

Can it take VCF from a GRCh38 analysis? Please suggest possible way to do.

maxh190 commented 3 years ago

Please take a look at the https://github.com/HGLab/VIC:

java -jar target/VIC-1.0.1.jar [-b ] [-d ] [-h] [-input_type ] [-i ] [-cancer_type ] [-convert2annovar ] [-l ] [-skip_annovar] [-o ] [-annotate_variation ] [-table_annovar ] [-s ] [-otherinfo ] [-db ]

-annotate_variation The Annovar perl script of annotate_variation.pl -b,--buildver The genomic build version, it can be hg19 and will support GRCh37 hg18 GRCh38 later

On Wed, Sep 22, 2021 at 5:01 AM praveenraj2018 @.***> wrote:

Can it take VCF from a GRCh38 analysis? Please suggest possible way to do.

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praveenraj2018 commented 3 years ago

Hi Max,

I saw that. That means currently hg38 is not supported and no new version is planned for hg38?

maxh190 commented 3 years ago

When you specify -b hg38, the VIC pipeline should lead the ANNOVAR package installed on your machine to download/install the hg38 resources.

praveenraj2018 commented 3 years ago

Ok. What about the vicdb files? Especially the genomic coordinates e.g. in civic file