Correcting deletion records presentation in VCF file.

Question

[rahimrajwani]

I have a VCF (v3.3) file which is presenting deletion records as:

Chromosome  334924  .   CGCCG   D5  49  0   NS=1;DP=30
Chromosome  334930  .   TCC D3  47  0   NS=1;DP=30
Chromosome  334950  .   A   D1  49  0   NS=1;DP=30
Chromosome  334968  .   T   D1  49  0   NS=1;DP=30
Chromosome  334996  .   GC  D2  46  0   NS=1;DP=30
Chromosome  335127  .   AA  D2  50  0   NS=1;DP=30
Chromosome  335177  .   A   D1  50  0   NS=1;DP=30
Chromosome  335223  .   AGA D3  48  0   NS=1;DP=30
Chromosome  335245  .   TT  D2  49  0   NS=1;DP=30

Now most of the tools out there are unable to interpret it correctly. Neither it seems to be the correct way to represent deletions. I have an idea how these should be presented as in VCF file specification. Given deletion records in this form, is there any tool or script that can help to convert to standard form?

I have tried to bcftools norm and vcf-convert. And also manually changing the field to "." It doesn't seem to be the solution.

Any ideas are highly appreciated. Thanks.