HailException: Invalid locus ‘3:198024579’ found. Position ‘198024579’ is not within the range [1-198022430] for reference genome ‘GRCh37’.
Is there a specific question? This is an invalid locus in GRCh37, so Hail won’t construct it. This error up front is probably saving you a headache later when you’re trying to make sense of results.
But why is this error occuring while applying VEP, my data is in build 37 so applying VEP for build 37 is giving me this error. It is not letting me apply VEP. What should i do.
Can it be that my vcf is corrupt?
Yes, this is very possible. The line of Hail code that triggers the error is not necessarily the module that is throwing the error, since Hail programs are lazy.
What is the full stack trace? I’m guessing this is actually happening on import_vcf.