Consider the following REF/ALT sequence pairs.
REF CTGTG------TGTGTGTGTGAAAA
ALT1 CTGTGTGTGTGTGTGTGTGTGAAAA
ALT2 CTGTGTGTGAGTGTGTGTGTGAAAA
=> Left-shifting ALT1
REF C------TGTGTGTGTGTGTGAAAA
ALT1 CTGTGTGTGTGTGTGTGTGTGAAAA
... leads to this variant.
C -> CTGTGTG at pos. 1
=> Left-shifting ALT2
REF CTGT------GTGTGTGTGTGAAAA
ALT2 CTGTGTGTGAGTGTGTGTGTGAAAA
... leads to this variant:
T -> TGTGTGA at pos. 4
This is problematic since in VCF notation, these two variants will result in two different
records. When using bcftools merge, instead of one insertion we suddenly have two -- all because
of a single-base error.
Moreover, when comparing VCF variants row by row between ALT1 and ALT2, we will not pick up that we actually have two mismatching variants rather than two independent insertions (we lose the information that ALT1 and ALT2 will be never present together).