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EBIvariation / vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11
Apache License 2.0
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Fields PL and GL now depend on the ploidy of GT #103

Closed Anishka0107 closed 6 years ago

Anishka0107 commented 6 years ago

Fixes #101

The VCF spec defines for GL : "In presence of the GT field the same ploidy is expected; without GT field, diploidy is assumed." It defines PL as : "The phred-scaled genotype likelihoods rounded to the closest integer, and otherwise defined precisely as the GL field."

This is probably not the case with other fields whose Number is G like GP, CNL, CNP, hence not implementing this for those.

Anishka0107 commented 6 years ago

Just adding a commit with partial work. Not yet ready for review!!

(Doesn't work and also has ugly code)