Comparing VCF files

In this post, I will compare different tools for comparing VCF files. To create a reproducible example, I will make use of Docker and Conda. I highly recommend learning about these tools if you haven’t already; they make it easier to reproduce your work. I have written some notes on Docker and Conda that maybe…

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Converting PED into VCF

Updated 2015 August 25th: as suggested by Tim, I checked out PLINK 1.9 and found it much simpler to convert PED into VCF. I updated the post with instructions for performing the conversion using PLINK 1.9. Being late to the game of analysing genomic variants, I only recently discovered that IGV is capable of visualising…

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