I have a question regarding bcftools norm ( bcftools norm Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows (Galaxy Version 1.9+galaxy1)).
Using the tool 6 variants in my vcf got realigned. However, for one of them it seems like the realignment is not the most left position according to the following definition:
„A VCF entry is left aligned if and only if its base position is smallest among all potential VCF entries having the same allele length and representing the same variant“ (Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics. https://academic.oup.com/bioinformatics/article/31/13/2202/196142 )
chr1: 115254052 C-CTC
chr1: 115254051 T -TCT
Here is a screenshot of the sequence (GRCh37) as presented in the Genome Data Viewer by NCBI.
Shouldn’t be the correct realigned position:
chr1: 115254050 G GTC
I am glad for any suggestions or explanations.
Thanks a lot!