Say I have two VCFs with 100 samples in each file. Each VCF was joint-called separately and now I want to merge the variant calls. 

Do I need to left-align the INDELs in the merged VCF? I've used `bcftools norm` in the past and got odd results. It seems that `vt` is a better tool for this. 

Is left-aligning only useful for common variants? If I'm interested in rare variants (<0.5% AF) would left-alignment actually matter? 

Thanks

Here's an example of bcftools norm

Original VCF

    chr7    157009949       .       AGCGGCGGCGGCG   AGCGGCGGCGGCGGCGGCG,A,AGCGGCGGCGGCGGCGGCGGCG,AGCGGCGGCG,AGCGGCGGCGGCGGCGGCGGCGGCG,AGCGGCGGCGGCGGCG


---

Left-Aligned VCF (with multiallelics split into biallelic calls)


    chr7    157009949       .       A       AGCGGCGGCG  
    chr7    157009949       .       A       AGCGGCGGCGGCG
    chr7    157009949       .       A       AGCGGCG
    chr7    157009949       .       A       AGCG
    chr7    157009949       .       A       AGCGGCGGCGGCGGCG   
    chr7    157009949       .       AGCG    A
    chr7    157009949       .       AGCGGCG A
    chr7    157009949       .       AGCGGCGGCGGCG   A


---



Suppose one of your VCF files has a non-left-aligned insertion, represented as REF=AG, ALT=AGT, starting at position 99999, and another file has an insertion represented as REF=G, ALT=GT, starting at position 100000.  If you don't left-align, these may not be recognized as the same variant, and downstream analysis will suffer.