Biallelic and Multiallelic explain

Question

[pinn]

Hi

After normalisation of a variants vcf by using Vt normalizer

Input - only one vcf file; hg38.fa (ref) The stats I got total no .of biallelic normalized - 3286 total no. of multiallelic normalized - 10 total no. of variants normalized - 3296 total no. of variants observed - 1934627

Can u give me detail explanation of biallelic and multiallelic means ?

Thanks!

Answer 1

[arta]

A biallelic site is a locus in a genome that contains two observed alleles, counting the reference as one, thus allowing for one variant allele.

On the other hand, a multiallelic site is a locus in a genome that contains three or more observed alleles (such as blood group in humans), counting the reference as one, thus allowing for two or more variant alleles.

[pinn]

Thanks! for example Ref - ATG
ALT- CGT is it called multiallelic ?

Is it possible to see bi and multialleic in a vcf file ?

[Ram]

That's an MNV - a multi-nucleotide variant, possible an InDel. A Multialleleic site is where at 1 locus (chr+pos), you see multiple ALT alleles. VCF displays multiple alleles using a , to separate the alleles. From GATK's forum, here's an example:

19 38875072 rs62123481 G A,C 2147568933.95 PASS .....(trimmed)

See the A,C in the ALT field? This means that at that locus (chr19:38875072), the caller sees 3 bases: the REF (G) and 2 ALTs: A and C