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Caveman outputting invalid VCF REF == ALT  #128

@mp15

Description

@mp15

##cavemanVersion=1.15.2

from pipeline seems to be outputting invalid VCF.

chr13 91186809 72b5bfd0-2806-11ef-a86d-095e775c607f C C . . DP=50;MP=1.4e-12;GP=1.0e+00;TG=CC/CCCCC;TP=1.1e-03;SG=AC/CCCCC;SP=1.0e+00 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0/0:0:7:0:0:5:4:0:0:6.9e-01 0/0:0:14:0:0:0:20:0:0:1.0e+00

In a valid VCF REF cannot == ALT if REF == ALT then ALT = . I’m not entirely clear what this entry is trying to communicate. If it’s supposed to be a subordinate line to an overlapping INDEL then the * allele would be the correct choice.

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