trouble converting imputev2 files to vcf file

Question

[SHN]

Hello All,

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!

[4galaxy77]

You are using 2 very outdated programs. They are both almost 10 years old. shapeit4 and impute5 are the most recent programs and much quicker / convenient to use and both use vcf/bcf, so no messing around with .haps files.

[SHN]

Very informative, thanks!

Answer 1

[SHN]

For those who are arriving here. This issue and confusion has been responded thoroughly in is it .impute2 format equal to .gen format

I eventually renamed all the data.impute-haps to data.impute.haps and used the data.impute.sample generated in the pre-phasing step with shapeit2 for to convert my files from IMPUTE2 output format to vcf format using SHAPEIT.