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VCF mining & interpretation tools (hg38 build)

i need recommendation for VCF mining & interpretation tools (hg38 build) like gemini but with hg38 support Kindly list any tools used in variant disease association and variant phenotype association or any tools of VCF statistics and analysis.

Regards elsayed

vcf annotation snp clinvar mining
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updated by Biostar Biostar • written by elsayedhegazy • elsayedhegazy

2 answers

Plink - https://www.cog-genomics.org/plink/1.9/

Hail - https://github.com/hail-is/hail

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written by pfs pfs

Hail seems great but i need standalone tool not based on Apache Spark any other recommendations ?

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written by elsayedhegazy • elsayedhegazy

To be clear, Hail doesn't require a cluster. And you can install it locally with Python 3 and pip install hail.

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written by jbloom • jbloom

Another option would be to use a tool like liftover to convert the VCF coordinates to hg19 coordinates and then using Gemini. Changing Genome Coordinates For Vcf

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written by pfs pfs

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