Is there any other file formats besides VCF that are commonly used to record genetic mutation events? I am trying to include more input format for my software. Thank you.
I consider VCF to be one of the worst formats ever "defined". I mean, it's not really even a format, considering that all of the useful data is custom-defined in the header, making it virtually impossible to parse. So, any other format you encounter is almost certainly better.
Complete Genomics' variant format was pretty good a while ago. But they've been bought by China now, so probably it's been corrupted.
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