Changes

This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the STR.

This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the STR.

Left alignment is usually a concept associated with Indels.  We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele).  Similarly, an indel representation can be non parsimonious as shown in the figure with the caveat that it is possible for the leftmost nucleotide to be the same in all alleles as it is a requirement that no empty alleles exists.

Left alignment is usually a concept associated with Indels.  We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele).   

 

Similarly, an indel representation can be non parsimonious as shown in the figure with the caveat that it is possible for the leftmost nucleotide to be the same in all alleles as it is a requirement that no empty alleles exists.

=== How to observe that a variant is not left aligned or parsimonious on the right side? ===

=== How to observe that a variant is not left aligned or parsimonious on the right side? ===