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VCF conservation into Treemix

I have a multi-sample vcf file with ~7 millions SNPs. Now I want to convert it into required format of the Treemix. I run it using vcf2treemix.sh along with plink2treemix.py, but plink2treemix.py works very very slow. So that if I use it, the analysis in question may take more than a month or even longer.

Does anyone of you have a solution to increase the speed of this program or a better suggestion to do this analysis

Thanks

treemix plink vcf
• 1,543 views • link
written by reza reza

I found the solution

population program from Stacks package

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written by reza reza

1 answer

It looks to me like a custom script, and without looking at the script code, it is difficult to suggest any solution. Would it help if you split your original VCF file into chromosome VCF files and then run your code on individual chromosome files and consolidate the output in single file?

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written by sure • sure

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