Reduce reference alternative to same position

Question

[roalva1]

Hello,

I have this four lines in a VFC:

9 4118205 CCGA CCGG
9 4118206 CGA CGG
9 4118207 GA GG
9 4118208 A G

At the end, all they are

9 4118208 A G

would you know if there is some tool (i.e. in bcftools) to reduce this?

Thank you very much

Answer 1

[Pierre Lindenbaum]

https://samtools.github.io/bcftools/bcftools.html

beftools norm

Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows.

[roalva1]

I saw this tool, but I thought it just does left align. Thanks!!