Question

VCF mining & interpretation tools (hg38 build)

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7.2 years ago

elsayedhegazy ▴ 30

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 • 2.2k views

ADD COMMENT • link updated 6.9 years ago by Biostar 20 • written 7.2 years ago by elsayedhegazy ▴ 30

score 1 · Answer 1 · 2017-09-20

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7.2 years ago

pfs ▴ 280

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

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

ADD COMMENT • link 7.2 years ago by pfs ▴ 280

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

ADD REPLY • link 7.2 years ago by elsayedhegazy ▴ 30

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

ADD REPLY • link 6.1 years ago by jbloom • 0

score 1 · Answer 2 · 2017-09-20

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7.2 years ago

pfs ▴ 280

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

ADD COMMENT • link 7.2 years ago by pfs ▴ 280