Recently I am using Annovar to annotate my gVCF file generated by GATK. I am confused with some lines：
chr6 31324208 31324208 G 0 exonic HLA-B chr6 31324493 31324494 CA 0 exonic HLA-B chr6 31324494 31324497 AGGT 0 exonic HLA-B
The Alt field is 0 instead of "-" for deletion and other characters for SNP. What does these "0" Alt mean? Thank you
Does not it mean, that alternative allele depth is zero? So it is mean, that you have only reference (ref) allele count? Can you copy/paste part of your gVCF?