Corey
by Corey
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  • Bioinformatics

InDel is a common concept in molecular biology, while the representation for InDels are non-unique. There are at least two representations: left-alignment and right-alignment. Actually, it does not really matter, but it good to have a convention. I would like to suggest using left-alignment for these reasons:

ref            : CGTATGATCTA [GCGCGC] TAGCTAGCTAGC
left-alignment : CGTATGATCTA [--GCGC] TAGCTAGCTAGC
right-alignment: CGTATGATCTA [GCGC--] TAGCTAGCTAGC
  1. Standard Statistical genetics center of the university of Michigan denotes that left-alignment is necessary.

  2. Community Most famous tools are stick to left-alignment, such as GATK, ANNOVAR and related databases:

  • avsnp138
  • avsnp142
  • clinvar_20150330
  • 1000g2014oct
  • exac03
  • esp6500siv2

The standard convention is to place an indel at the left-most position possible. —GATK

Since left-normalization is gaining more and more popularity, my suggestion is to just use left-normalization, and that database curators as well as users both use this practice, so that we can compare apples to apples. —ANNOVAR

In the end, I would prefer to stick to the convention — left-alignment.