No valid chromosomes found! on Michigan Imputation Server

Question

[graeme.thorn]

I have two vcf files - one hg19 and one hg38, analysing data from the same participants on two slightly different SNP platforms. Both files have been through the pre-imputation checks.

The header (and the first line) of the hg38 version looks like:

##fileformat=VCFv4.3
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20230906
##source=PLINKv2.00 
##contig=<ID=chr1,length=248917420>
##contig=<ID=chr2,length=242106609>
.. other contigs
##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 <participant_IDs so removed>
chr22   15349056    22:15349056:C:T C   T   .   .   PR  GT  0/0 0/0 0/0 0/0 0/0 ...
...

The hg19 version looks like:

##fileformat=VCFv4.3
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20230906
##source=PLINKv2.00 
##contig=<ID=1,length=249211619>
##contig=<ID=2,length=243048760>
.. other contigs
##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 <participant_IDs so removed>
22  16590657    22:16590657:T:C T   C   .   .   PR  GT  0/1 0/0 0/0 0/1 0/0 ....
...

Both files have the chromosome identifiers recommended by MIS (hg19: <X>, hg38: chr<X>), but both files are failing the initial validation with No valid chromosomes found!

What could be causing this issue? I could re-do the pre-imputation checks, but these have already been through them before they got to me.

I have ensured that the correct assembly is selected when trying to impute, and I have also tried both files with the "wrong" identifiers (chr<X> for hg19, <X> for hg38), but the jobs still fail this initial check.

[bk11]

Looks like you have correct format. You can try getting rid of alleles attached to SNP column (for e.g. change 22:16590657:T:C into 22:16590657) if that is the problem OR try running pre-imputation check again.

[graeme.thorn]

I've successfully run another dataset through MIS with identifiers that look similar <X>:<POS>:REF:ALT, so I don't think it's that

Answer 1

[graeme.thorn]

Turns out that running the pre-imputation checks again solved the issue, although I don't see how.