You must specify a region in the format chr, chr:start or chr:start-end at perl5/5.32/site_perl/Bio/DB/HTS/Tabix.pm line 104 about ensembl-vep HOT 3 CLOSED

Hi @xmy1990,

Hope you are well?
Thank you for your query

If possible can you share the VCF file used so we can try to recreate this issue, also to figure out if the issue is the input file, can you run VEP using this input file and the --assembly GRCh37.

Hoping to hear from you soon.
Thank you
Ola.

from ensembl-vep.

The same error exists with this vcf：https://github.com/Ensembl/ensembl-vep/blob/release/111/examples/homo_sapiens_GRCh37.vcf

For this error: “You must specify a region in the format chr, chr:start or chr:start-end at perl5/5.32/site_perl/Bio/DB/HTS/Tabix.pm line 104”, did it mean the #CHROM in my vcf did not have "chr" or other region?

My vcf like this:
chr1 86282 . T G 82.19 PASS AC=1;AF=0.00066;AN=1516;BaseQRankSum=1.121;DP=4113;Dels=0.00;FS=4.450;HRun=0;HaplotypeScore=0.1230;InbreedingCoeff=-0.0713;MQ=50.47;MQ0=377;MQRankSum=-0.472;QD=15.00;ReadPosRankSum=-0.047;SB=-31.80;VQSLOD=5.1323;pop=ALL
chr1 86331 rs115209712 A G 15414.55 PASS AC=218;AF=0.12616;AN=1728;BaseQRankSum=-4.790;DB;DP=4696;Dels=0.00;FS=0.922;HRun=2;HaplotypeScore=0.1808;InbreedingCoeff=0.0185;MQ=58.01;MQ0=1;MQRankSum=-7.246;QD=11.72;ReadPosRankSum=1.185;SB=-5186.86;VQSLOD=5.4426;pop=ALL

from ensembl-vep.

Hi,
I spent a day to debug the above, but unsolved.

“You must specify a region in the format chr, chr:start or chr:start-end at perl5/5.32/site_perl/Bio/DB/HTS/Tabix.pm line 104”,
What Tabix.pm in the error operates on? the hg38 ref fasta, my custom database, or anything else.

Thanks~

from ensembl-vep.