Suppose I have the following sequences with SNPs in 4th and 9th columns:
IND1 GATATTCGGA- IND2 GATGTTCTGAA IND3 GATATTCGGA- IND4 GATATTCGGAA IND5 GATGTTCTGAA IND6 GATGTTCTGAA
Haplotypes from such sequences would be:
AG- (2/6) GTA (3/6) AGA (1/6)
So far so good.
Now commonly I have a PED file which only contains SNP's. Using my example above columns with only SNPs would be:
AC- GTA AG- AGA GTA GTA
(actually the last column is not a SNP column but I hope is irrelevant because I have only SNPs as input)
So haplotyping is just a matter of counting and grouping equal sequences?
Where is the "haplotype inference" really?