For NGS analysis, the convention is to left align indels. To use GATK and samtools, you should use an aligner that left aligns indels; otherwise at least samtools will have worse performance and accuracy. It is too late to fix the issue in VCF.

EDIT: wait.. In your example, the two callers deleted different bases. The two calls are intrinsically different. You cannot move the indel to make them the same.

I suggest taking a look at vt. It includes a very nice left alignment routine. They've got a nice paper describing the method for normalizing the representation: http://bioinformatics.oxfordjournals.org/content/31/13/2202

There is the "vcf norm" tool in htscmd which left-aligns and normalizes indels in VCFs. It can be downloaded from github, google for 'htslib'.

a) Create a reversed reference genome b) Create a tool that reverse variants alleles .. and changes position (subtrack length_of_chrom +1- vcf_pos) c) Use a left-normalizing/shifting tool. d) use step b) again.

Voila.. Right shifting tool. Will post once I have it done.