vt cannot retrieve sequences from my reference sequence file

[alrafaykhan]

Deleted the reference index file.
Downloaded reference genome from the UCSC database.
But still getting the same error.
vt normalize HF.final.vcf.gz -r ref/hg19.fasta -o normalizeHF.final.vcf.gz

[variant_manip.cpp:72 is_not_ref_consistent] failure to extract base from fasta file: AL123456:24697-24715
FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file

[atks]

AL123456 is not a chromosome in hg19.fasta I believe. You should use the reference that was used to generate your VCF file.

[alrafaykhan]

After downloading the reference genome from ncbi genome still getting the same error
wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.fna.gz

vt normalize HF.final.vcf.gz -r ref/GRCh37_latest_genomic.fna.gz -o normalizeHF.final.vcf.gz

[variant_manip.cpp:72 is_not_ref_consistent] failure to extract base from fasta file: 1:866510-866510
FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file

[atks]

@alrafaykhan

GRCh37_latest_genomic.fna.gz has its chromosomes not named consistently with the chromosomes in your VCF file. They are prepended with NC_, NW_ and NT_.

You need to use a reference file where the sequences have a name consistent with what is found in your VCF file.

[vappiah]

@atks I had a similar issue. Below is is my error
[variant_manip.cpp:96 is_not_ref_consistent] reference bases not consistent: chr10:4868478-4868486 TGCGGGGCG(REF) vs Tgcggggcg(FASTA)

When I used the -n flag vt skipped several variants