Imputation server failing to see samples in VCF files

Question

[Ben]

I used the following command to generate VCF files from the 23andMe zip file for the Michigan Imputation server but it keeps failing with the validation error: At least 20 samples must be uploaded.

java \
  -jar vcf-tools-0.1.jar \
  vcf-generator \
  --in 23_n_me/23andme-tools-output/genome_name_v4_Full_20230822212500.zip \
  --ref human_g1k_v37.fasta \
  --out 23_n_me/23andme-tools-output/For_Imputation/ \
  --exclude Y,MT

The command spits out VCF.gz file for each chromosome which looks something like the following.

##fileformat=VCFv4.2
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  genome_name_v4_Full_20230822212500
1   734462  rs12564807  G   A   .   .   .   GT  1/1
1   752721  rs3131972   A   G   .   .   .   GT  1/1
1   838555  rs4970383   C   A   .   .   .   GT  1/1
1   861808  rs13302982  A   G   .   .   .   GT  0/1
1   873558  rs1110052   G   T   .   .   .   GT  0/1
1   889159  rs13302945  A   C   .   .   .   GT  1/1
1   891945  rs13303106  A   G   .   .   .   GT  1/1
1   894573  rs13303010  G   A   .   .   .   GT  1/1
1   909238  i6060381    G   C   .   .   .   GT  1/1
1   918384  rs13303118  G   T   .   .   .   GT  1/1
1   924898  rs6665000   C   A   .   .   .   GT  1/1
1   927309  rs2341362   T   C   .   .   .   GT  1/1
1   928836  rs9777703   C   T   .   .   .   GT  1/1
1   948692  rs2341365   G   A   .   .   .   GT  1/1

Would you know what might be wrong or if I am missing something? Is the output VCF format wrong?

[Andresa Raquel Capodifoglio]

Hi, how are you?
I'm encountering the same problem and would like to know how to combine the 25 samples to perform imputation.

Thank you so much in advance!

Answer 1

[bk11]

Your vcf file has only 1 sample, right? It cannot impute for only 1 sample. You need to have at least 25 samples for imputation.