I have searched all around the internet, and it really bothers me that I do not get it.
Chromosome position REF ALT type chr4 12345 A A 0/0 / = unphased, | = phased chr5 43473 A T 0/1 or 1/0 chr6 34384 G T,C 1/2 # multiallelic site with 2 alternative bases chr7 74549 ? ? 1/1
Could you help me understand what `1/11 means in the vcf output?
In here, it says:
the sample is a homozygous alternate
This basically means the base in the REF genome is the variant.
and they give as an example for
To me, that looks like
1/0 type. Can someone explain me why this
1/1 and how on earth this related
- The sample is a homozygous alternate --> there is no homozygosity
- This basically means the base in the REF genome is the variant. ---> How on earth the base of the REF is the variant? What is the then the base on the sample?