ambj
commented
6 years ago Dear Fredie Thank you for sending the VCF file to my email - this makes the trouble shooting allot simpler.
In the VCF headers the following is stated:
liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)
liftOverFile=/home/yudi/hg38_18/liftover_chain/hg38ToHg19.over.chain.gz
new_reference_genome=/home/yudi/hg19_chr/mergefa/hg19.chr.fa
It seems that your file indeed have been generated with the GRCh38 reference but then lifted ocer to the HG19 reference. For this reason you need to use the liftover option on the webserver to revert it back to GRCh38 again.
I can see that the error message form VEP is confusing - i have therefore added a more explanatory error message which will hopefully help guiding future similar problem.
Best, /AM
Hi,I used web server and got this error.
ERROR: VEP output file empty VEP Can't use an undefined value as a symbol reference at /home/tuba/shared/bin/ensembl-tools-release-85/scripts/variant_effect_predictor/variant_effect_predictor.pl line 2473, line 507.I don't know what's wrong with my vcf.It's obtained from Mutect2.I noticed that it can run by choosing submit Hg19... option.I'm pretty sure my reference genome is hg38.Is it my format or something else that has gone wrong?chrY 56734819 . C G . . DP=26;ECNT=2;NLOD=3.56;N_ART_LOD=-8.451e-01;POP_AF=5.000e-08;P_CONTAM=1.283e-05;P_GERMLINE=-5.786e+00;TLOD=6.19 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/0:12,0:9.553e-03:11,0:1,0:0:142,0:0:0:0|1:56734819_C_G 0/1:10,2:0.215:4,2:6,0:38:142,145:38:20:0|1:56734819_C_G:0.172,0.00,0.167:0.015,0.032,0.953 chrY 56734828 . T A . . DP=26;ECNT=2;NLOD=3.61;N_ART_LOD=-1.141e+00;POP_AF=5.000e-08;P_CONTAM=9.876e-06;P_GERMLINE=-5.645e+00;TLOD=6.17 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/0:12,0:0.071:11,0:1,0:0:142,0:0:0:0|1:56734819_C_G 0/1:9,2:0.209:4,2:5,0:37:134,145:38:29:0|1:56734819_C_G:0.182,0.00,0.182:0.017,0.030,0.953