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Michigan imputation server error

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.

topmed vcf
• 5,025 views • link
updated by Joel Wallenius Joel Wallenius • written by AR • 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

• 0 views • link
written by AR • AR

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

• 0 views • link
written by Kevin Blighe Kevin Blighe

2 answers

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

• 0 views • link
written by Kevin Blighe Kevin Blighe

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

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written by AR • AR

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

• 0 views • link
written by Kevin Blighe Kevin Blighe

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">

...

• 0 views • link
written by gebk • gebk

The HRC panel does not have chromosome Y, and it does not have the mitochondrial genome. The entire job fails because one or both of these vcf files fail the pipeline. Exclude them.

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written by Joel Wallenius Joel Wallenius

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