Question: Receive An Error In Fastphase Result
gravatar for mary
7.7 years ago by
Bologna university
mary210 wrote:

hello all

I try to estimated haplotype reconstruction by fastPHASE software. my data is SNP genotype of chromosome 14 for 5 cattle breed. I have 400 to 1000 animal for each breed and approximately 1000 genotype for each animal in chr. 14 (after filtration). when I run the command with whole data for one breed:

./fastPHASE -T10 -F -oMyresult mydata.inp

the program will be killed , but when I did it with a few animal (SNP genotype in whole chr. 14 for 5 animal) its worked and give me a file with name Myresult_freqs that contains a haplotype and frequency and S.E . but i can not do it for a few animal because of take several time and the result my be not correct compare with whole population result. i don't know why it dose not work for whole data (actually my data isn't very large)? based on fastPHASE manual it should do analysis for large data, I think my be I did some thing rang, is there any one that work with fastPHASE and had result for big data?

thanks for your consideration

data • 1.8k views
ADD COMMENTlink modified 7.0 years ago by Biostar ♦♦ 20 • written 7.7 years ago by mary210

1000 SNPs in 1000 individuals shouldn't be a problem. Maybe you can post the error message?

ADD REPLYlink modified 7.0 years ago • written 7.0 years ago by Fabio Marroni2.5k
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