I am trying to annotate a variant file(generated using strelka) from mice WGS data. This is the command I used:

    ./vep -i /path/to/somatic.snvs.vcf \
            --cache /data/shayantan/mus_musculus/ \
            --species mus_musculus  

The output variant file has no gene names. Why is this happening? Something wrong with my cache files?

EDIT (@Ram): Sample input VCF:

    #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
    chr1	3003110	.	G	T	.	LowEVS	SOMATIC;QSS=17;TQSS=1;NT=ref;QSS_NT=17;TQSS_NT=1;SGT=GG->GT;DP=35;MQ=60.00;MQ0=0;ReadPosRankSum=1.95;SNVSB=3.58;SomaticEVS=0.80	DP:FDP:SDP:SUBDP:AU:CU:GU:TU	18:0:0:0:0,0:0,0:17,17:1,1	14:0:0:0:0,0:0,0:11,13:3,4
    chr1	3035137	.	G	A	.	LowEVS	SOMATIC;QSS=17;TQSS=2;NT=ref;QSS_NT=17;TQSS_NT=2;SGT=GG->AG;DP=70;MQ=40.40;MQ0=10;ReadPosRankSum=0.89;SNVSB=3.23;SomaticEVS=0.10	DP:FDP:SDP:SUBDP:AU:CU:GU:TU	27:0:0:0:3,7:0,0:24,28:0,0	27:0:0:0:4,6:0,0:23,29:0,0
    chr1	3035168	.	C	T	.	LowEVS	SOMATIC;QSS=8;TQSS=2;NT=ref;QSS_NT=8;TQSS_NT=2;SGT=CC->CT;DP=51;MQ=47.72;MQ0=3;ReadPosRankSum=1.78;SNVSB=2.68;SomaticEVS=0.08	DP:FDP:SDP:SUBDP:AU:CU:GU:TU	18:0:0:0:0,0:16,19:0,0:2,4	23:0:0:0:0,0:20,25:0,0:3,3
    chr1	3035504	.	C	A	.	LowEVS	SOMATIC;QSS=15;TQSS=2;NT=ref;QSS_NT=14;TQSS_NT=2;SGT=CC->AC;DP=59;MQ=51.03;MQ0=2;ReadPosRankSum=-1.19;SNVSB=2.71;SomaticEVS=0.09	DP:FDP:SDP:SUBDP:AU:CU:GU:TU	23:0:0:0:3,5:20,22:0,0:0,0	27:0:0:0:4,4:23,28:0,0:0,0
    chr1	3043000	.	G	T	.	LowEVS	SOMATIC;QSS=21;TQSS=1;NT=ref;QSS_NT=21;TQSS_NT=1;SGT=GG->GT;DP=53;MQ=46.60;MQ0=7;ReadPosRankSum=1.70;SNVSB=1.37;SomaticEVS=0.20	DP:FDP:SDP:SUBDP:AU:CU:GU:TU	20:0:0:0:0,0:0,0:18,24:2,3	22:0:0:0:0,0:0,0:18,22:4,4

[Those variants are all intergenic][1]. There is no gene symbol because no genes are hit.

EDIT (@genomax) - Actual answer is further below in this chain at https://www.biostars.org/p/331209/#331504


  [1]: http://www.ensembl.org/Mus_musculus/Tools/VEP/Ticket?tl=F9VQxvXxHkzscTq9