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Santy-8128 / Minimac3

Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
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invalid syntax #7

Closed cariaso closed 7 years ago

cariaso commented 7 years ago

The fix from https://github.com/Santy-8128/Minimac3/issues/3 and https://github.com/Santy-8128/Minimac3/pull/6 is now being seen in the wild, but produces a syntactically invalid VCF. Both

https://github.com/jamescasbon/PyVCF (which promethease.com depends upon) and https://github.com/vcftools/vcftools (another industry standard parser)

both reject these two lines

FILTER=

FILTER=

with error messages like Syntax Error in your file: One of the FILTER lines is malformed: ##FILTER=

in files that I've seen from independent sources.

cariaso commented 7 years ago

appears to be addressed by https://github.com/Santy-8128/Minimac3/commit/42aa451443a592900be079a34963960bdca003f7