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Converting SNP Data to Biallelic Allele Format with awk

Learn how to transform SNP data from numeric format to biallelic letter allele format efficiently using `awk`, especially for large datasets. --- This video is based on the question https://stackoverflow.com/q/63783769/ asked by the user 'Kwame Oduro' ( https://stackoverflow.com/u/550566/ ) and on the answer https://stackoverflow.com/a/63784811/ provided by the user 'thanasisp' ( https://stackoverflow.com/u/7589636/ ) at 'Stack Overflow' website. Thanks to these great users and Stackexchange community for their contributions. Visit these links for original content and any more details, such as alternate solutions, latest updates/developments on topic, comments, revision history etc. For example, the original title of the Question was: Changing snps in 00, 11, 20 in a file to biallelic letter allele using another file which has the nucleotides as map file Also, Content (except music) licensed under CC BY-SA https://meta.stackexchange.com/help/l... The original Question post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/... ) license, and the original Answer post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/... ) license. If anything seems off to you, please feel free to write me at vlogize [AT] gmail [DOT] com. --- Converting SNP Data to Biallelic Allele Format with awk When working with genetic data, particularly SNP (single nucleotide polymorphism) information, researchers often encounter raw data files that present genetic variants in numeric formats. For example, data columns may indicate counts of alleles using numeric representation (like 00, 11, 20). However, for most applications, it's essential to represent these SNPs in their respective biallelic letter formats, often referred to as ACGT (Adenine, Cytosine, Guanine, Thymine). In this guide, we will guide you through a practical solution for transforming the SNP data from a numeric format to a biallelic letter allele format using awk. Let's dig deeper into this problem and explore the solution step by step. Understanding the Problem The task involves two primary files: raw.txt: Contains genetic information where certain columns represent SNPs in numeric format. snp.txt: Acts as a mapping file that associates each SNP with its corresponding alleles — both minor and major. Example Data Here’s a simplified look at what the data in each file resembles: raw.txt: [[See Video to Reveal this Text or Code Snippet]] snp.txt: [[See Video to Reveal this Text or Code Snippet]] Desired Output The output wants the biallelic representation of the SNPs, for example: [[See Video to Reveal this Text or Code Snippet]] The Solution The proposed solution to achieve the desired output is through an awk script tailored to read both files and apply the necessary transformations. Here is a detailed breakdown of the approach. The Awk Script The following awk script allows you to dynamically handle any number of SNP columns, accommodating files with a larger dataset (for instance, over 65,000 SNPs). Here’s the step-wise breakdown of the script: [[See Video to Reveal this Text or Code Snippet]] Explanation of the Code Mapping SNPs: The first block processes the snp.txt file and populates a hash table (snp) that maps the SNP identifiers combined with their numeric allele counts to the corresponding biallelic allele sequences. Each unique combination of SNP and count (20, 11, 00) is stored. Reading Header: The second block captures the header from raw.txt and stores the column names starting from the 7th field (SNP columns) in an array called col. Transforming Data: In the last block of the script, each SNP column is updated based on the mappings found earlier. For each column from the 7th to the last, the numeric value is replaced with its corresponding biallelic representation. Usage To execute the awk script on your files, use the command line as follows: [[See Video to Reveal this Text or Code Snippet]] This command will read both files and generate the output.txt file containing the transformed biallelic representations of the SNPs. Conclusion Transforming SNP data from a numeric format to a biallelic representation can significantly enhance data interpretation in genetic studies. Using the flexibility of the awk programming language, we’ve equipped you with a robust solution that seamlessly handles both small and extensive datasets. By applying this method, researchers can efficiently process and analyze genomic data, leading to more accurate insights in genetic research. This approach should help you manage your SNP data more effectively, so whether you manage thousands or even hundreds of thousands of SNPs, your tasks have just become much easier! Happy coding!