Changes

Left aligning a variant means shifting the start position of that variant to the left till it is no longer possible to do so.  It is a concept associated with insertion and deletion variants.  In order to further differentiate left alignment from simply left padding a variant, the definition is as follows:

Left aligning a variant means shifting the start position of that variant to the left till it is no longer possible to do so.  It is a concept associated with insertion and deletion variants.  In order to further differentiate left alignment from simply left padding a variant, the definition is as follows:

     A variant is left aligned if it is no longer possible to shift its position to the left while keeping the length of all alleles constant.  The colour of the text is synchronized to the variant it is describing in the figure,

     A variant is left aligned if it is no longer possible to shift its position to the left while keeping the length of all alleles constant.   

The following figure shows examples of an unnormalized short tandem repeat which is a special class of indels.

The following figure shows examples of an unnormalized short tandem repeat which is a special class of indels. The colour of the text is synchronized to the variant it is describing in the figure.

* <span style="color:#ff0000">The representation of variants in a VCF file requires that no alleles in the REF and ALT field are represented with an empty string (empty allele). The red indel is an illegal VCF representation.</span>

* <span style="color:#ff0000">The representation of variants in a VCF file requires that no alleles in the REF and ALT field are represented with an empty string (empty allele). The red indel is an illegal VCF representation.</span>