Question: how to find haplotype of SNPs
0
gravatar for khatami.mahshid
7 months ago by
khatami.mahshid20 wrote:

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?

snp • 204 views
ADD COMMENTlink modified 7 months ago by colindaven2.4k • written 7 months ago by khatami.mahshid20

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

ADD REPLYlink written 7 months ago by curious440

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?

ADD REPLYlink written 7 months ago by khatami.mahshid20

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

ADD REPLYlink written 7 months ago by curious440

try haplo.stat in R?

ADD REPLYlink written 7 months ago by Jimbou770
0
gravatar for colindaven
7 months ago by
colindaven2.4k
Hannover Medical School
colindaven2.4k wrote:

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.

ADD COMMENTlink written 7 months ago by colindaven2.4k
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