https://github.com/weinstockj/filter_somatic_variants_gwas_topmed

A collection of Go scripts to create a database of potential somatic artifacts in the TOPMed germline calls.
https://github.com/weinstockj/filter_somatic_variants_gwas_topmed

bioinformatics golang gwas-summary-statistics

Last synced: about 2 months ago
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A collection of Go scripts to create a database of potential somatic artifacts in the TOPMed germline calls.

• Host: GitHub
• URL: https://github.com/weinstockj/filter_somatic_variants_gwas_topmed
• Owner: weinstockj
• Created: 2020-07-23T02:08:25.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2023-01-02T05:49:05.000Z (about 2 years ago)
• Last Synced: 2024-06-21T08:04:26.726Z (7 months ago)
• Topics: bioinformatics, golang, gwas-summary-statistics
• Language: Go
• Homepage:
• Size: 4.88 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
A short Golang script for filtering GWAS summary statistics based on two sources of blacklisted variants:

1. Variants are putative somatic variants based on recurrent somatic variant calling

2. Variants that based on their quality metrics, may be somatic 

This script has been used with application to TOPMed GWASes where we want to prune out all somatic variants.

contact Josh Weinstock with questions.