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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
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Invalid GT in Gaps #68

Open tseemann opened 3 years ago

tseemann commented 3 years ago 
[E::vcf_parse_format] Couldn't read GT data: value not a number or '.' at NZ_NGSV01000001:1
NZ_NGSV01000001 1       .       A       <*>     0       Gaps    END=3   GT:GQ:DP:AD
     *:*:*:*

For Gap GT=. and DP=0 and GQ=. and AD=.` ?

tseemann commented 3 years ago

In fact, I think it is OK for different rows to have different INFO lines.

So Gaps could just have GT:DP. .:0

hsinnan75 commented 3 years ago

I've changed ::: to .:.:0:. If it does not work, please let me know. Thank you very much!