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awk-n-bash
This page will contain useful awk one-liners and bash constructs. Example 1: Add up all values in a column Example 2: If/else, passing bash variables to awk, combining columns from two files Example 3:...
View Articleawk to subset records based on IDs from a different file
I recently had to extract 400 non-contiguous records from a tab-delimited file that contained ~25K records, each with ~199K columns. In this case, the file contained genetic data for ~199K SNPs, for...
View ArticleCreating a snptable for genetic imputation (when you don’t have GenomeStudio)
Here I describe how to create a SNPtable to use gengen’s convert_bim_alleles.pl tool. This tool is used to convert SNP notation from manufacturer-specific format (e.g. Illumina’s 1/2 or TOP/BOT...
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