Run Variant Effect Predictor on vcf file - Githubissues

genophenoenvo / terraref-datasets

Repository for code and small datasets derived from the TERRA REF program

MIT License

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Run Variant Effect Predictor on vcf file #7

Closed dlebauer closed 3 years ago

dlebauer commented 4 years ago

Pankaj suggested that we annotate the variants from this combined VCF file: http://datacommons.cyverse.org/browse/iplant/home/shared/terraref/genomics/derived_data/bap/resequencing/danforth_center/version1/hapmap.

One option is to use the SnpEff application, it is contained in the discovery environment and described here: https://wiki.cyverse.org/wiki/display/DEapps/Variant+annotation+using+SnpEff+in+DE
Another option is to use the ensembl-vep https://uswest.ensembl.org/info/docs/tools/vep/index.html tool

dlebauer commented 4 years ago

@MagicMilly please link to the vcf file in the phenotypes readme

dlebauer commented 3 years ago

old and out of date