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Post-imputation steps (cleaning and converting to plink)

Hi,

I have just finished imputing my genetic data on the Michigan server (filtered on r2=0.3) and I want to convert to plink. What are the next steps such as cleaning and converting to plink? Anyone have any useful scripts and to do this over all chromosomes?

Any advice would be much appreciated!

Thanks

snp michigan imputation server
• 4,491 views • link
written by kl • kl

Hmmm.. I've found some commands to annotate and convert to plink. However, the output is definitely not a correct plink .bim file! I tried to also just convert into plink without annotating (in case that caused it) but the same thing happens. the second column is chr:pos:A1:A2:snp or chr:pos:A1:A2 (without the annotation step). Do you have any idea why this may happen?

plink --vcf chr22_rs.vcf --keep-allele-order --double-id --make-bed --out test

22      22:16053843:G:A;rs181029838     0       16053843        A       G
22      22:16054839:G:A;rs73877820      0       16054839        A       G
22      22:16055207:C:T;rs7291810       0       16055207        T       C
22      22:16055230:T:C;rs140593956     0       16055230        C       T
22      22:16055965:G:T;rs587706951     0       16055965        T       G

Thanks

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updated by GenoMax GenoMax • written by kl • kl

The files downloaded from the Michigan server are v4.1 using minimac4.

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written by kl • kl

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

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written by GenoMax GenoMax

I think I've tried that before but couldn't get it work as it needs a C++ library which I couldn't seem to install. I'll try and see if I can figure it out if its the only way to convert! Thanks for the advice.

• 0 views • link
written by kl • kl

Please post the error about the C library, if possible. Generally, working with these genetics programs is a tiring affair.

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written by Kevin Blighe Kevin Blighe

Yes, I'm not tech-savvy so it makes it even more tiring! So, I've closed it into my directory using Git and then, the next step is downloading cget. I do this in the directory of DosageConvertor (not sure if this is what is needed but it is unclear)

pip install cget

Requirement already satisfied: cget in /home/kl/.local/lib/python3.7/site-packages (0.1.9)
Requirement already satisfied: six>=1.10 in /cm/shared/languages/anaconda3-2019.10/lib/python3.7/site-packages (from cget) (1.12.0)
Requirement already satisfied: click>=6.6 in /cm/shared/languages/anaconda3-2019.10/lib/python3.7/site-packages (from cget) (7.0)

Then I type bash install.sh and I have the following message:

/cm/shared/languages/anaconda3-2019.10/bin:/cm/shared/apps/Python-Meep-1.3/bin:/cm/shared/apps/openmpi/gcc/64/1.6.5/bin:/cm/shared/languages/Python-2.7.6/bin:/cm/shared/languages/GCC-4.8.4/bin:/cm/shared/tools/git-2.22.0/bin:/cm/shared/languages/GCC-7.1.0/bin:/cm/shared/apps/moab/7.2.9/sbin:/cm/shared/apps/moab/7.2.9/bin:/cm/shared/languages/GCC-6.1/bin:/cm/shared/languages/R-3.6.2/bin:/cm/shared/apps/Java-JDK-11.0.3/jdk-11.0.3/bin:/cm/shared/languages/GCC-9.1.0/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/cm/shared/apps/Plink2:/cm/shared/apps/Bolt-LMM-2.3/BOLT-LMM_v2.3:/cm/shared/apps/bcftools-1.8/bcftools:/cm/shared/apps/bcftools-1.8/htslib-1.8:/cm/shared/apps/Tabix-0.2.6/tabix-0.2.6:/sbin:/usr/sbin:.:/cm/shared/apps/torque/4.2.4.1/bin:/cm/shared/apps/torque/4.2.4.1/sbin:/cm/shared/apps/hdf5/1.6.10/bin:/cm/shared/libraries/gnu_builds/gsl-1.16/bin)
Error: cget not installed. Please run 'pip install --user cget'

So, I am not sure what I've done wrong!

Thanks for your help!

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updated by Kevin Blighe Kevin Blighe • written by kl • kl

1 answer

Surely Michigan Imputation Server has information on this? In which format do they produce data?

I have an entire pre-phasing and imputation workflow, here (but not via Michigan): C: Phasing with SHAPEIT

Kevin

• 0 views • link
written by Kevin Blighe Kevin Blighe

Hmmm.. I've found some commands to annotate and convert to plink. However, the output is definitely not a correct plink .bim file! I tried to also just convert into plink without annotating (in case that caused it) but the same thing happens. the second column is chr:pos:A1:A2:snp or chr:pos:A1:A2 (without the annotation step). Do you have any idea why this may happen?

plink --vcf chr22_rs.vcf --keep-allele-order --double-id --make-bed --out test

22      22:16053843:G:A;rs181029838     0       16053843        A       G
22      22:16054839:G:A;rs73877820      0       16054839        A       G
22      22:16055207:C:T;rs7291810       0       16055207        T       C
22      22:16055230:T:C;rs140593956     0       16055230        C       T
22      22:16055965:G:T;rs587706951     0       16055965        T       G

Thanks

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updated by Ram Ram • written by kl • kl

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

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written by Ram Ram

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