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Dear all,<br>
<br>
I have installed on my machine your recent vep API locally to use a
home made genome in order to get SNPs annotations.<br>
<br>
I used the instructions on these pages:<br>
<a class="moz-txt-link-freetext"
href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#offline">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#offline</a><br>
<a class="moz-txt-link-freetext"
href="http://www.ensembl.org/info/docs/tools/vep/script/index.html">http://www.ensembl.org/info/docs/tools/vep/script/index.html</a><br>
<br>
My inputs are:<br>
-> a home made reference genome in fasta file<br>
-> a .VCF file with SNPs list on that genome<br>
-> a .GTF file with genome annotations<br>
<br>
My goal is to use vep to generate a .vep file with functionnal
annotations of my SNPs.<br>
<br>
For instance:<br>
<br>
my gtf is:<br>
tig00000004_pilon_pilon Pacbio gene 231183 234374
. + . gene_id "A"; <br>
tig00000004_pilon_pilon Pacbio transcript 231183
234374 . + . gene_id "A";transcript_id "A"; <br>
tig00000004_pilon_pilon Pacbio CDS 231183 234374 .
+ . gene_id "A";transcript_id "A"; <br>
tig00000004_pilon_pilon Pacbio exon 231183 234374
. + . gene_id "A";transcript_id "A"; <br>
<br>
( I also tried with a .gff)<br>
<br>
my vcf is:<br>
##...<br>
#CHROM POS ID REF ALT QUAL FILTER INFO
FORMAT A_ATTACTCG <br>
tig00000004_pilon_pilon 232205 . G A 9881.15
.
AC=8;AF=0.800;AN=10;DP=245;FS=0.000;MLEAC=8;MLEAF=0.800;MQ=60.05;QD=25.82;SOR=0.983
GT:AD:DP:GQ:PL 0:9,0:9:99:0,247 <br>
<br>
=> this snp should be found in the gene "A"<br>
<br>
To prepare the gtf (or also .gff), I used:<br>
grep -v "^#" test.gtf | sort -k1,1 -k4,4n -k5,5n | bgzip -c >
test.gtf.gz<br>
tabix -p gtf test.gtf.gz<br>
<br>
my command line is:<br>
./vep -i test.vcf -gtf test.gtf.gz -fasta ref.fasta
--force_overwrite<br>
or <br>
./vep -i test.vcf -gff test.gff.gz -fasta ref.fasta
--force_overwrite<br>
<br>
The result file is:<br>
#Uploaded_variation Location Allele Gene Feature
Feature_type Consequence cDNA_position CDS_position
Protein_position Amino_acids Codons
Existing_variation Extra<br>
. tig00000004_pilon_pilon:232205 A - -
- <b> intergenic_variant</b> - - -
- - - IMPACT=MODIFIER<br>
variant_effect_output.txt (END)<br>
<br>
<br>
It does not work, it retreives only integenic variants which is
wrong as I have some SNPs in genes...<br>
<br>
When I try the tools on data that I used to work on using gtf2vep.pl
a few years ago, it does not work either....<br>
<br>
Could you please help me and tell me if I am doing something wrong?<br>
<br>
Thank you in advance.<br>
<br>
Best regards,<br>
<br>
Sabrina
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