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andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
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Number entry in VCF header #72

Open GuilhemSempere opened 6 years ago

GuilhemSempere commented 6 years ago

Hi

Version 0.8.1 of Platypus generates the following header lines:

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

I agree that according to VCF specs, the number entry has to be "." for GL since it is a list of values. However wouldn't it be more accurate to set it to "1" for GQ, GOF, NR and NV, just as for GT?

G.

GuilhemSempere commented 6 years ago

Sorry my question only makes sense for GOF and GQ since NR and NV contain one value per allele

tdelhomme commented 6 years ago

I think that following the VCF specifications, this should be an "A" (one value per alternate allele). At the moment this creates a bug if using vt for example, as it uses this number/value to know into how many fields it should divide the site (decompose mode).