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!