imputed dosage to vcf
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Entering edit mode
3 months ago
rheab1230 ▴ 30

Hello, I am trying to convert my imputed dosage file from michigan imputation server to vcf format. I tried to use 2 softwares: dosageconvertor and dose2vcf tools But I am getting error in both. For dose2vcf: the command used: .

/dose2vcf_v0.5

the error:

-bash: ./dose2vcf_v0.5: Permission denied

I downloaded the file using this command: https://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM

wget http://csg.sph.umich.edu//cfuchsb/dose2vcf_v0.5.gz

And for dosageconvertor: I am getting error during installation process: the step followed is:

cd DosageConvertor bash install.sh mkdir build && cd build cmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake .. make

But I am getting error: make

make: Warning: File 'Makefile' has modification time 3632 s in the future
make[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 3632 s in the future
make[2]: Warning: File 'CMakeFiles/DosageConvertor.dir/flags.make' has modification time 3632 s in the future
Scanning dependencies of target DosageConvertor
make[2]: warning: Clock skew detected. Your build may be incomplete.
make[2]: Warning: File 'CMakeFiles/DosageConvertor.dir/flags.make' has modification time 3632 s in the future
[ 33%] Building CXX object CMakeFiles/DosageConvertor.dir/src/HaplotypeSet.cpp.o
[ 66%] Building CXX object CMakeFiles/DosageConvertor.dir/src/Main.cpp.o
[100%] Linking CXX executable DosageConvertor
/home/miniconda3/envs/train/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/miniconda3/envs/train/lib/libz.so: undefined reference to memcpy@GLIBC_2.14' /home/miniconda3/envs/train/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/miniconda3/envs/train/lib/libstdc++.so: undefined reference to aligned_alloc@GLIBC_2.16'
/home/miniconda3/envs/train/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/kxj190026/miniconda3/envs/train/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/DosageConvertor.dir/build.make:101: DosageConvertor] Error 1
make[1]: *** [CMakeFiles/Makefile2:73: CMakeFiles/DosageConvertor.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

Does anyone know how to deal with this or know of any other tool to convert imputed dosage file from michigan server to vcf format.

vcf impute dosage plink conversion • 166 views
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