how to find haplotype of SNPs

Question

[khatami.mahshid]

Hi all,

I have these format of SNPs: "0/0" "0/1" "1/1"

I know the ref/alt alleles. for these SNPs and for specific donors how can I find out haplotypes?

for example, if my donors were like these :

---

donor1:

SNP1 - SNP2 - SNP3

0/0 - 0/1 - 0/0

---

donor2:

SNP1 - SNP2 - SNP3

0/1 - 0/1 - 0/0

---

how can I find out the haplotypes?

[curious]

How many SNPs/samples do you have? If I understand your problem right statistical phasing software can achieve this.

[khatami.mahshid]

I have 3 SNPs and 450 samples. my problem is more about what "0/1" should be considered? I know it is ref/alt but I got confused that which one is in haplotype? ref or alt?

[curious]

In VCF specification 0 is ref. I'm not sure if you can phase with 3 SNPs, somebody else will know though

[Jimbou]

try haplo.stat in R?

Answer 1

[colindaven]

If you have short reads (eg not Pacbio/Nanopore) phasing results are likely to be very, very poor, as no long range information (long reads) are available.