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FORMAT/CNL example has Number=G, should be Number=. ? #806

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eroller opened this issue Jan 28, 2025 · 0 comments
Open

FORMAT/CNL example has Number=G, should be Number=. ? #806

eroller opened this issue Jan 28, 2025 · 0 comments
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@eroller
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eroller commented Jan 28, 2025

The FORMAT/CNL field has Number=G according to:

##FORMAT=<ID=CNL,Number=G,Type=Float,Description="Copy number genotype likelihood">

but the field as described below seems to be in conflict:

CNL specifies a list of $log_{10}$ likelihoods for each potential copy number, starting from zero.

I think the Number=G means the number of possible GT values that can be formed from the alleles (REF and ALT)? When using allele specific copy number alleles then there may be more than one possible GT for a given total copy number value.

Perhaps the Number=G should be changed to Number=.? And the same would go for CNP?

@jkbonfield jkbonfield added the vcf label Jan 28, 2025
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