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how long is haplotype estimation?

ulipkin

Community Trekker

Joined:

Dec 17, 2014

hi,

i stoped  a haplotype estimation of above 200k snps after 24 hours. is it taking so long or am i missing sonething?

2 REPLIES
kelci_miclaus

Joined:

May 27, 2014

How large is the sliding window size you are using for estimating haplotypes?  This process uses the EM algorithm to estimate haplotypes across a window size of markers.  It can become extremely computationally intensive with large numbers of markers, especially if you are attempting to create large windows sizes of haplotypes.  It is not unusual for this to have long run times.

ulipkin

Community Trekker

Joined:

Dec 17, 2014

Thanks. I used the default window size of 5 SNPs with no overlap.