Python Script For Calculating Private SNPs
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21 months ago
ThePlaintiff ▴ 70

Does anyone have a link to a python script for calculating population private SNPs? Many articles indicate that ad-hoc scripts were used to obtain private SNPs but the code or the algorithm summary is always unavailable. I know about bcftools isec and vcftools isec. I'd like to have a look at the Python implementations. I have vcf_files for every population that I'm interested in.

SNP • 702 views
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Why does it need to be python? You can use bcftools AND make the exact command available for others to reproduce. Having a custom python code doesn't make things any better.

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Thanks for your response. It doesn't have to be in Python. The code may be written in C/C++, BASH, Java or R. I'm interested in reviewing the implementations. Private SNPs are defined differently by different articles e.g https://www.pnas.org/content/112/11/3439.long and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3498066/. I just thought that there would be code samples in the wild or algorithm summaries. I know that writing a Python wrapper for bcftools should be simple using the os.system module and other equivalents.

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Why does any language need to be involved? I'm saying that if bcftools can do it, do the task with bcftools and include the command so the task can be reproduced.

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I apologize if my question is a little obscure. I was hoping to get an algorithmic summary or code examples on how private SNPs are calculated. I'm inclined to believe that there are resources that can satisfy my request online. I can both ran bcftools and write a wrapper that calls bcftools from Python. I'm just interested in how the calculation is done.