Variant calling
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!
1 answer
GATK will report multi-nucleotide variants (MNVs) but these are not terribly common. Those entries can also make it difficult to compare VCFs.
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Jeremy Leipzig
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