Question

VEP output has no gene names

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6.3 years ago

Gene_MMP8 ▴ 240

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

alignment sequencing vep • 5.0k views

ADD COMMENT • link updated 18 months ago by barslmn ★ 2.3k • written 6.3 years ago by Gene_MMP8 ▴ 240

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Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

You're using vep. A vep tag would help your cause.

ADD REPLY • link 6.3 years ago by Ram 44k

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Thanks for editing my code. I will surely keep this in mind for future posts.

ADD REPLY • link 6.3 years ago by Gene_MMP8 ▴ 240

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I think you need to add the option --symbol to the command.

ADD REPLY • link 6.3 years ago by 162916 • 0

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Thanks. But even after including --symbol, I am getting no gene names

ADD REPLY • link 6.3 years ago by Gene_MMP8 ▴ 240

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instead of cache, can you run the code with db option for few selected variants? @ banerjeeshayantan

ADD REPLY • link 6.3 years ago by cpad0112 21k

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Please can you show us a sample of your input file.

ADD REPLY • link 6.3 years ago by Emily 24k

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#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

ADD REPLY • link updated 6.3 years ago by Ram 44k • written 6.3 years ago by Gene_MMP8 ▴ 240

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Hey! You said you'd keep the editing tip in mind for future posts. Use the code formatting to your advantage, man :-)

ADD REPLY • link 6.3 years ago by Ram 44k

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This is so embarrassing. I was in a hurry and so couldn't format it. I will surely follow the site's guidelines form the next post.

ADD REPLY • link 6.3 years ago by Gene_MMP8 ▴ 240

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18 months ago

LayneSadler ▴ 90

Include the --symbol argument

Adds the gene symbol (e.g. HGNC) (where available) to the output. Some gene symbol, e.g. HGNC, are only available in merged cache and therefore should be used with --merged option while using cache to get result. Not used by default

http://useast.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_symbol

ADD COMMENT • link 18 months ago by LayneSadler ▴ 90

GenoMax · Accepted Answer · 2018-08-07

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6.3 years ago

Emily 24k

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

EDIT (@genomax) - Actual answer is further below in this chain at C: VEP output has no gene names

ADD COMMENT • link updated 6.3 years ago by GenoMax 147k • written 6.3 years ago by Emily 24k

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chr1    3930912 .   G   A   .   LowEVS  SOMATIC;QSS=2;TQSS=1;NT=ref;QSS_NT=2;TQSS_NT=1;SGT=GG->GG;DP=26;MQ=58.54;MQ0=0;ReadPosRankSum=-1.85;SNVSB=1.53;SomaticEVS=1.26;ANN=A|intergenic_region|MODIFIER|Xkr4-Rp1|Xkr4-Rp1|intergenic_region|Xkr4-Rp1|||n.3930912G>A||||||   DP:FDP:SDP:SUBDP:AU:CU:GU:TU    16:0:0:0:0,0:0,0:16,16:0,0  9:3:0:0:2,5:0,0:4,5:0,0

Here in spite of being an intergenic variant, it has a gene name. I am confused.

ADD REPLY • link 6.3 years ago by Gene_MMP8 ▴ 240

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Are you using an up-to-date version of the VEP? What is your reference genome? That variant is coming up as intronic to a lincRNA for me.

ADD REPLY • link 6.3 years ago by Emily 24k

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My reference genome is mm9. I am using an older reference as the bam files were aligned and the variants were called using this reference genome only. The vep version is ensemble-vep 93.2

ADD REPLY • link 6.3 years ago by Gene_MMP8 ▴ 240

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Are you using the Ensembl release 67 cache files? Or your own custom cache? What was in the input line for that variant?

ADD REPLY • link 6.3 years ago by Emily 24k

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I used the cache file from this page under the mouse genome and column known as "variation vep". This resulted in opening of a page from where I downloaded the mus_musculus_vep_93_GRCm38.tar.gz file.Did I do anything wrong?

ADD REPLY • link 6.3 years ago by Gene_MMP8 ▴ 240

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That cache is GRCm38 (mm10). You're using NCBI37 (mm9). Of course it doesn't work.

ADD REPLY • link 6.3 years ago by Emily 24k

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Thanks for pointing it out. If possible, Can you please direct me to the appropriate link?

ADD REPLY • link 6.3 years ago by Gene_MMP8 ▴ 240

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This is not the easiest problem. You will need to use the NCBIm37 cache from Ensembl 67, which will probably not work with the current VEP, and will work best with VEP 67.

VEP 67

NCBIm37 cache

Your alternative would be to run your VCF files through the Ensembl Assembly Converter to get them onto GRCm38, but be aware that you may lose some data this way.

ADD REPLY • link 6.3 years ago by Emily 24k

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Thanks for suggesting the steps. I will try it out. This really helped! Thanks again.

ADD REPLY • link 6.3 years ago by Gene_MMP8 ▴ 240

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Please accept Emily's answer.

ADD REPLY • link 6.3 years ago by Ram 44k

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Hi again. The VEP 67 version link is down. Are you aware of any active links?

ADD REPLY • link 6.3 years ago by Gene_MMP8 ▴ 240

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Not down for me - I can access the link.

ADD REPLY • link 6.3 years ago by Ram 44k

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Hello Emily! I am working with the cattle genome. How can I add gene name in vep output?

ADD REPLY • link 3.7 years ago by brianaloredana ▴ 30

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Use --symbol with the offline VEP. Online, tick Gene symbol (should be selected by default). With the REST API it should be enabled by default.

ADD REPLY • link 3.7 years ago by Emily 24k