Dear all Could you please explain the meaning of this 2/0 2/1 2/2 also 3/0 3/1 3/2 imagine that I have
CHROM POS REF ALT ALT1
1 2078 A ACACAC ACAC
You can give an example from you to illustrate that.
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stat.1405 •
0: Reference
1: Alternate allele
2: Second alternate allele
3: Third alternate allele
So 2/0 is ACAC/A and 2/1 is ACAC/ACACAC. You only have two alternate alleles shown, so there should be no 3/? in there. This is basically a modified VCF format.
so if I have a third alt allele for example G. 3/1 will be G/A 3/2 will be G/ACAC 3/3 will be G/G so if I have more than tow alleles there is no Homzygous in REF,
3/1 would be G/ACACAC, 3/2 would be G/ACAC and so on. It's always possible to have a homozygous reference allele, regardless of the number of alternate alleles.
thank you so much
Note that in a valid VCF the ALT1 column would not exist, so your example would not be correct.
According to the VCF format specification, all the Alternate alleles are defined in the "ALT" column, separated by commas.
For example, your example would be:
CHROM POS REF ALT
1 2078 A ACACAC,ACAC
In this case, a genotype of 1 would mean ACACAC, and a genotype of 2 would represent ACAC.
In general, SNPs should always be bi-allelic variations, e.g. only two alleles are commonly found. In the close past, tri-allelic SNPs were generally filtered out, in order to simplify he downstream analysis. However, recently I've seen some tri-allelic SNPs being used in public datasets, so this may create some confusion in the future.
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