Gene mutations as a binary variable
Is there as easy way to get particular genes at the individual levels as a binary variable (mutant vs not)?
Is there as easy way to get particular genes at the individual levels as a binary variable (mutant vs not)?
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Hi Sara,
No, there is no easy way to find that. For specific SNPs that are covered by the Genotyping data, there is a Notebook https://github.com/UK-Biobank/SNP-filtering and a forum post https://community.ukbiobank.ac.uk/hc/en-gb/community/posts/18669657313437-How-do-I-extract-allele-combinations-at-specific-SNPs-using-Jupyterlab that might help. For specific SNPs in the Whole Exome Sequencing data the Genomics search in the Cohort Browser can be used to select all the participants that are homozygous or heterozygous for a particular mutation.
Please note that the Genotyping positions are in GRCh37, whereas the WES and WGS positions are in GRCh38.
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