problem with chromosomes in michigan imputation server

Question

[jfertaj]

Hi,

I am trying to impute a dataset using the Michigan imputation server but I got this error:

No valid chromosomes found!

I have vcf (with tabix index) files from 1-23 chromosomes that look like this:

Should I add chr at the beginning?

##fileDate=20170710
##source=PLINKv1.90
##contig=<ID=9,length=141077353>
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  1A073_C08_100811_1A073  1A223_A05_100811_1A223  1A224_1A224     1A226_A11_100811_1A226  1A242_H09_100811_1A24
9       205764  rs10811213      C       T       .       .       PR      GT      0/0     0/1     0/0     0/0     0/1     0/0     0/0     0/0     0/1     0/0     0/0     0/0     0/1
9       212189  rs9406775       C       T       .       .       PR      GT      0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0
9       213149  rs680654        G       A       .       .       PR      GT      0/0     0/1     0/0     0/1     0/1     0/0     0/1     0/1     0/0     1/1     0/0     ./.     0/0
9       214864  rs2236547       C       T       .       .       PR      GT      0/0     0/1     0/0     0/0     0/1     0/0     0/0     0/0     0/1     0/0     0/0     0/0     0/1
9       215269  rs636922        A       C       .       .       PR      GT      0/0     0/1     0/0     0/1     0/1     0/0     0/1     0/1     0/0     1/1     0/0     1/1     0/0
9       215494  rs7869327       C       T       .       .       PR      GT      0/0     0/1     0/0     0/0     0/1     0/0     0/0     0/0     0/1     0/0     0/0     0/0     0/0
9       215511  rs2023402       C       T       .       .       PR      GT      0/0     0/1     0/0     0/0     0/1     0/1     0/0     0/0     1/1     0/0     0/0     ./.     0/0
9       215534  rs635615        C       T       .       .       PR      GT      0/0     0/1     0/0     0/1     0/1     0/0     0/1     0/1     0/0     1/1     0/0     1/1     0/0
9       216124  rs561921        A       G       .       .       PR      GT      0/1     0/0     1/1     0/1     0/0     0/1     0/0     0/0     0/0     0/0     0/1     0/0     0/0
9       217269  rs598791        A       G       .       .       PR      GT      0/0     0/1     0/0     0/1     1/1     0/0     0/1     0/1     0/0     1/1     0/0     1/1     0/0
9       217397  rs529045        G       A       .       .       PR      GT      0/0     1/1     0/0     0/1     1/1     0/0     0/1     0/1     0/1     1/1     0/0     1/1     0/1
9       224693  rs601023        C       T       .       .       PR      GT      1/1     0/0     0/1     0/1     0/0     0/1     0/1     0/1     0/1     0/0     1/1     0/0     0/1
9       227621  rs4740661       C       T       .       .       PR      GT      0/0     0/1     0/0     0/0     0/1     0/0     0/0     0/0     0/1     0/0     0/0     0/0     0/1
9

[WouterDeCoster]

Should I add chr at the beginning?

That's one of the most common issues in bioinformatics, so it's always a safe bet to try if it solves your issue.

[dbaranger]

I was encountering the same problem. Adding 'chr' to the chromosomes (ie. '--output-chr chr26' in plink) didn't seem to resolve this. Instead, '--output-chr M' fixes the issue for me. Which is a bit silly, since chromosomes are listed as numbers in both the 'M' and '26' formats, but I guess there's a difference.

[Dan]

I split the file into chromosomes, I changed the chromosome name to chr1 and updated the contig line in the header, I bgzip'ed the file and passed all the checks from the vcf debugulator: https://github.com/EBIvariation/vcf-validator

The server still throws an uninformative error: unfortunately, your job failed.

Weirdest of all, the spinner next to the section that reads Input Validation -> Analyze file blah-01.vcf.gz... is still spinning away... I'm not sure if the job has /actually/ failed or not :(

Answer 1

[mgru]

It's because of your chromosome X- it only accepts an X as X rather than 23. Set it via plink and then resubmit.

Answer 2

[Dan]

4.6 years ago and no answer?

[Dan]

Using 1 works, using chr1 doesn't work.

[gebk]

New user here. I'm encountering the same problem. Where do you add the 'chr1' in the vcf file?

Answer 3

[Samuel Brady]

Yes, adding on "chr" may help. I'm not sure what program you are running, but if one of your program's inputs is a reference fasta file and it has ">chr1" format chromosome names instead of ">1" then adding "chr" will help.

Answer 4

[binodregmi30]

the server takes chr1 or 1 depending on genomic built