Sanger Imputation Service - The input file sanity check failed

Question

[alesssia]

Dear all,

I would like to impute a genotype dataset using the Sanger Imputation Service. I created the VCF file using PLINK (v1.90) and, as suggested in the Sanger website. checked its validity using several tools (namely: vcf-validator, included in vcftools, bcftools stats and checkVCF) and no errors have been pointed out. However, when I submit it to the Imputation Service, I get the following error:

--- Aborted Job ---

 The input file sanity check failed, "bcftools norm -cs" exited with the following message:
        [fai_fetch_seq] The sequence "23" not found

        faidx_fetch_seq failed at 23:2710157

Des anyone has a clue about what is generating the problem? The VCF is in format 4.2

Thank you very much!

Answer 1

[Pierre Lindenbaum]

Change the chromosome column: change 23 to X, 24 to Y ...

[alesssia]

Thanks Pierre. It seems that now it is working!