Michigan imputation server error

Question

[AR]

I am trying to upload my vcf files on Michigan imputation server. I have a single vcf file containing genotype data. I used these commands:

bgzip example.vcf
tabix example.vcf.gz
tabix -l example.vcf.gz | parellel -j 5 'tabix -h  example.vcf.gz {} > {}.vcf'

It generated separate chromosome.vcf files (1..22, X, Y, MT). Again I used bzip to obtain zip files for uploading. I tried to upload all 25 files (chromosome.vcf.gz files:1..22, X, Y, MT) all together to the server and got the error

Error : No valid chromosomes found!

If I am uploading single vcf.gz file of single chromosome, it is working perfectly fine.

Can anyone figure out what is the issue here. I am not able to understand. How can I solve it. How can I upload my all vcf.gz files for all chromosomes together as it is really very annoying to upload single single file every time.

Any help would be really appreciated.

[AR]

Hi Kevin

Thank you very much for your help. I was able to solve the issue. I just added 'chr' in my chromosome.vcf.gz files and it did the trick!

I am able to upload my 22 chromosome files + X chromosome file. But it is not recognising my Y chromosome file. Again giving me same error:

Error : No valid chromosomes found!

Thanks

AR

[Kevin Blighe]

Great that you got it working. chrY may not be supported - I am not sure.

Answer 1

[Kevin Blighe]

Please take a look at the comments and answers in this previous thread, and try the solutions suggested: problem with chromosomes in michigan imputation server

Also note: https://imputationserver.readthedocs.io/en/latest/prepare-your-data/

Kevin

[AR]

Hi Kevin,

Thanks for the reply.

I am bit confused about the imputed genotype quality check. As I have used minimac4 for imputation, I can use r-square for quality check of my imputed data. Other than this, I am not able to find any other parameter. Can you pls refer me to some article where I can have more additional parameters for post-imputation QC specifically for minimac4 imputed data. I have already performed pre-imputation QC (sample and SNP QC). Once I am done with QC part (post-imputation), I can go ahead with association analysis.

Thanks

AR

[Kevin Blighe]

I have not used minimac - sorry. I suggest contacting the authors of the program.

[gebk]

Hi AR, did you solve it? I have the same problem and same error. Where exactly did you add "chr' in the files? Thank you so much.

The header looks like this.

...

CHROM=<ID=UNKNOWNCHR, Number=1, Type=String, ...

FORMAT=

FILTER=<ID=PASS,Description="Annotated by SNP QC as the best and recommended probeset for the marker.">

FILTER=<ID=FAIL,Description="Annotated by SNP QC as not the best and recommended probeset for the marker.">

contig=<ID=1>

...

contig=<ID=MT>

FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

...