Bimbam can not open panel phased HapMap data file when imputing genotypes

[Andrew]

Hi folks,

I tried to impute genotypes in a gene region for some SNPs not on Affy
6.0 SNP chip.

I use the following commands in Bimbam

./bimbam –g my.geno.txt –p my.pheno.txt –pos mySNP.pos –g
hap.phased.cnj.b36.chr3.inp –p 0 –pos hap.phased.cnj.b36.chr3.pos

-gene mygene.txt –GF 10000 –wmg 0 –o impute


But error shows can not open genotype-file:
hap.phased.cnj.b36.chr3.inp

Anybody helps me with this?


Thanks,

Andrew

[Yongtao Guan]

If there is a log file being generated, could you send it to me? What
OS are you using?
Could you check if the hap.phased.cnj.b36.chr3.inp in the same
directory as bimbam?

Grant

--
Yongtao Guan, PhD
Postdoctoral Fellow
Dept of Human Genetics
University of Chicago
http://home.uchicago.edu/~ytguan/