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Hi Will,<br>
<br>
Thanks for your answer.<br>
How important is the biotype for the predictions ?<br>
<br>
Best regrads,<br>
<br>
Sabrina<br>
<br>
<div class="moz-cite-prefix">Le 22/05/2017 18:02, Will McLaren a
écrit :<br>
</div>
<blockquote
cite="mid:CAMVEDX0wG+6Wggx4=DoNq_JU_geMWu89jHxHQfe9NE5DtJXFMQ@mail.gmail.com"
type="cite">
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<div dir="ltr">Hi Sabrina,
<div><br>
There's a few issues with your GTF; if you correct them then
it should work.</div>
<div><br>
</div>
<div>1) IDs should not be shared by transcripts and genes. In
your example, I fixed this by prefixing the gene ID with "g_"
and the transcript ID with "t_"</div>
<div><br>
</div>
<div>2) Transcript entries need a valid biotype; typically this
will be "protein_coding" (see <a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#gff">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#gff</a>)</div>
<div><br>
</div>
<div>3) The phase field must be correctly set for CDS entries.</div>
<div><br>
</div>
<div>These points also apply if you use a GFF format file.</div>
<div><br>
</div>
<div>Hope that helps</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 22 May 2017 at 12:36, Sabrina
Legoueix-Rodriguez <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:sabrina.legoueix@inra.fr" target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:sabrina.legoueix@inra.fr">sabrina.legoueix@inra.fr</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> 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 moz-do-not-send="true"
class="m_5616784093623879695moz-txt-link-freetext"
href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#offline"
target="_blank">http://www.ensembl.org/info/<wbr>docs/tools/vep/script/vep_<wbr>cache.html#offline</a><br>
<a moz-do-not-send="true"
class="m_5616784093623879695moz-txt-link-freetext"
href="http://www.ensembl.org/info/docs/tools/vep/script/index.html"
target="_blank">http://www.ensembl.org/info/<wbr>docs/tools/vep/script/index.<wbr>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=<wbr>0.000;MLEAC=8;MLEAF=0.800;MQ=<wbr>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:<wbr>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
<a moz-do-not-send="true" href="http://gtf2vep.pl"
target="_blank">gtf2vep.pl</a> 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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