Using GATK pipeline, I am getting indels with no additional information in the other columns in the VCF file. One thing is that if there is no information available for a variant, the column is filled with a dash( and the additional columns are not just blank). But the indels which I am talking about have just blank columns for the additional info fields.
So, my question is whether those indels are some false positives reported by GATK or there can be variants with such blank columns in the VCF output?
Thanks in advance