Is it posible obtain a Cohort with all the Pathogenic Variants in a gene? Former User of DNAx Community_2 26 August 2022 00:00 3 comments Comments 3 comments Sort by Date Votes Ondrej Klempir DNAnexus Team 12 September 2022 11:42 1) There is a recent thread showing the Hail functionality and how to analyze genomics data using Hail:https://community.dnanexus.com/s/question/0D5t0000043xrVhCAI/hail-tutorial-and-example-notebooks-for-ukbrap-analysis This is the place I would start with, in order to implement more advanced geno filters and export eids of such cohorts. https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/gwas_ann_vep.ipynb 0 Ondrej Klempir DNAnexus Team 12 September 2022 11:53 2) Depending on what "Pathogenic Variants" annotation means, in the Cohort Browser, there is a possibility to apply a geno filter: You can then specify Variant Effects (e.g. High) and Genes/Genomic range. This cohort could be then explored on GENOMICS tab and exported as a new cohort: 0 Former User of DNAx Community_2 15 September 2022 17:17 Thank You! This is very helpful 0 Please sign in to leave a comment.
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1) There is a recent thread showing the Hail functionality and how to analyze genomics data using Hail:
https://community.dnanexus.com/s/question/0D5t0000043xrVhCAI/hail-tutorial-and-example-notebooks-for-ukbrap-analysis
This is the place I would start with, in order to implement more advanced geno filters and export eids of such cohorts.
https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/gwas_ann_vep.ipynb
2) Depending on what "Pathogenic Variants" annotation means, in the Cohort Browser, there is a possibility to apply a geno filter:
Thank You! This is very helpful
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