[ensembl-dev] Inconsistence output result found between running by cache and remote database

[Kenneth Wong]

The scenario is described as below :
1. input.vcf :
   ##fileformat=VCFv4.0
   #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
   2       31754395        .       C       T       .       .       .

2. Execute below commands with versions 92

 /* Run VEP by connecting to remote Ensembl DB */
  ./vep -i  input.vcf -o vep-online.out\
  --fork 4 --buffer_size 100\
  --refseq --assembly "GRCh37"\
  --database --port 3337 --db 92\
  --hgvs --numbers --symbol --flag_pick --no_stats\
  --species homo_sapiens\
  --fields $VEP_FIELDS

 /* Run VEP via local cache */
  ./vep -i input.vcf -o vep-cache.out\
  --fork 4 --buffer_size 1000\
  --offline --cache --dir_cache $VEP_CACHE_DIR\
  --refseq --fasta ~/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa\
  --hgvs --numbers --symbol --flag_pick --no_stats\
  --species homo_sapiens\
  --fields $VEP_FIELDS\
  --use_given_ref

, where
$VEP_FIELDS=Uploaded_variation, Location, Allele, Gene, SYMBOL,
SYMBOL_SOURCE, HGNC_ID, Feature, Consequence, Protein_position,
Amino_acids, Codons, HGVSc, HGVSp

$VEP_CACHE_DIR=~/.vep/cache/

3. Below discrepancies are found between the output file "vep-cache.out"
and "vep-online.out" (as attached)

vep-cache.out :
- Amino_acids = R/Q
- Codons = cGa/cAa
- HGVSp = NP_000339.2:p.Arg227Gln

vep-online.out :
- Amino_acids = E/K
- Codons = Gag/Aag
- HGVSp = NP_000339.2:p.Glu227Lys

Assume the result in vep-cache.out is correct, would you please advice
what's wrong in the parameters when running VEP via remote database?

Many thanks for your help!

Kenneth Wong
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