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This is the code behind the www.impute.me site. It contains algorithms for imputing personal genomes, as well as a range of custom-made analysis for genetics-based disease and health.

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gene-surfer

##Imputation algorithm description

The imputation is performed by three functions from functions.R as well as a cron-job named imputation_cron_job.R

The three functions are

prepare_23andme_genome which is triggered at data-submission time (not cron-job dependent). This function simply unpacks the data, copies it to the designated imputation area (~/imputations), performs a few data consistency checks and assigns an unique id to each submission.

run_imputation is triggered by the cron-job checking for ready data in the imputation area (~/imputations). It consists of a series of calls to bash-based programs. First a shapeit call is made to phase the data correctly. Note that there is quite a lot of extra work involved in avoiding errors from single-sample-homozygote problems and such (up untill the cmd4 call). After shape-it calls, a call to impute2 is made and the end-product of this function is per-chromosme gen-files entitled "step_7_chr_xx", because they come from the seventh step of calculation.

summarize_imputation is run immediately after run_imputation, in the cron-job, and could probably be merged into this function. The goal of this function is to organize and summarize the per-chromosome gen-files: saving as 1) a gen-file with probability-estimate-containing imputation data, and 2) a '23andme'-format file in which the calls are already made. The current threshold is 0.9, per the gtools default setting. Note that there's a lot of splitting taking place to minimize the memory footprint, which could otherwise become very large, particularly for the long chromosomes.

The caller function is this script file

imputation_cron_job.R (a script file in the imputeme folder). This file calls the two cron-job driven functions. The extra code in the file is used to determine if it should run as a hub-job or a node-job; node jobs are prefered, because they the cron-job driven imputation functions are computationally expensive.

##Module design description.

Each module consists of a ui.R and a server.R file. The details of the setup of this can be found in the R/Shiny documentation. A template module which contains the very minimal configuration is found in the 'template' folder.

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This is the code behind the www.impute.me site. It contains algorithms for imputing personal genomes, as well as a range of custom-made analysis for genetics-based disease and health.

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