Variant calling

Question

[Anst]

Hello!

I am wondering if a situation which I will describe below can be real.

If a string of nucleotides of my interest is AGTTA and the reference is AAAAA, after variant calling could I have SNPs like A\A is pos 2, for example? Or I could only have a combination of bases in the fixed position?

Maybe I missed the algorithm of calling, it would be nice if you tell me about it in simple words.

Thanks!

Answer 1

[Jeremy Leipzig]

GATK will report multi-nucleotide variants (MNVs) but these are not terribly common. Those entries can also make it difficult to compare VCFs.