I have a vcf file, which I want to upload on the Sanger Imputation server. The following error occured:
--- Aborted Job --- The input file sanity check failed, "bcftools norm -ce" exited with the following message: Reference allele mismatch at X:3155141 .. REF_SEQ:'T' vs VCF:'G'
As suggested by the sanger website, I wanted to solve this issue with the bcftools +fixref command.
All my SNPs have dbsnp-IDs, so I downloaded the following file for reordering alleles:
When I now use the
bcftools +fixref broken.vcf -O z -o fixref.vcf -- -d -f /path/to/reference.fasta -i `All_20151104.vcf.gz`
command, the following error appears:
[E::bgzf_uncompress] Inflate operation failed: invalid distance too far back [E::bgzf_read_block] Invalid BGZF header at offset 15203091877
It seems, that the All_20151104.vcf.gz file is corrupted. I also am not able to index it with bcftools. However, another operation (subsetting it to regions) works...
Does anyone know, how to solve this problem?