problem with chromosomes in michigan imputation server
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
4 answers
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.
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Samuel Brady
the server takes chr1 or 1 depending on genomic built
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binodregmi30 •
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That's one of the most common issues in bioinformatics, so it's always a safe bet to try if it solves your issue.
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.
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 :(