gVCF questions with "0" in the Alt field

Question

[ccma]

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

[Paul]

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?

[Medhat]

I think

Sites inside of heterozygous deletions are altered to have haploid genotype entries (e.g. "0" instead of "0/0", "1" instead of "1/1").

more

Answer 1

[ccma]

Thank you all. I am new to biostars. I don't known how to post my results properly either the table or the screenshot. I will try my best to illustrate this question.

Fro example: "chr6 31324208 31324208 G 0 exonic HLA-B"

The position is at : chromosome 6 ,start at 31324208 , end at 31324208 The reference is: G The alternative is: "0" instead of "-" any other characters (Here is the question part) The mutation is an exonic mutation The gene symbol is HLA_B

Others like:"chr3 38534292 38534296 CACAT 0 UTR3 ACVR2B NM_001106:c.9469_9473delins0 "

It seems like a deletion of AVVR2B gene, the reference is "CACAT", the alternative is "0"

Hope the question is clear.

[Paul]

Please edit your original question and do not post additional information as an answer.