I can not figure out what I am doing wrong. I prephased my data using shapeit and imputed my data against 1000G phaseIII using -phase option.
./impute2 \ -use_prephased_g \ -m ./Example/example.chr22.map \ -h ./Example/example.chr22.1kG.haps \ -l ./Example/example.chr22.1kG.legend \ -known_haps_g ./Example/example.chr22.prephasing.impute2_haps \ -int 20.4e6 20.5e6 \ -Ne 20000 \ -o ./Example/example.chr22.one.phased.impute2 -phase
The output files are as below:
file file_allele_probs file_haps file_info file_info_by_sample file_summary file_warnings
I am trying to convert data files using shapeit
shapeit -convert --input-haps file --output-vcf file.vcf
And it tells me there is no .haps file. and then it needs a
.sample file which I don't have in my output file.
Can anyone direct me what I am doing wrong? What I am missing? I know I should be having a
.haps file but I don't get this file and imputed results are saved in a separate folder.
Appreciate any hints!