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<p>Dear Lucas,</p>
<p>It looks like your GFF file is missing some entries with the
following IDs (these IDs are also present in the attribute
"Parent" of other child entries in your GFF file):</p>
<p>PF3D7_0108400.1,PF3D7_0108400.2, PF3D7_0105400.1,PF3D7_0105400.2,
PF3D7_0205700.2,PF3D7_0205700.1, PF3D7_0216700.1,PF3D7_0216700.2,
PF3D7_0210100.1,PF3D7_0210100.2, PF3D7_0208700.1,PF3D7_0208700.2,
PF3D7_0219400.2,PF3D7_0219400.1, PF3D7_0206900.1,PF3D7_0206900.2,
PF3D7_0202600.1,PF3D7_0202600.2</p>
or these entries have a "type" (gene, CDS, mRNA, exon, etc ..) not
supported by the VEP.<br>
Here is the list of "type" supported by the VEP tool: <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#gfftypes">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#gfftypes</a>
(click on the link "[Show supported types]").
<p>Best regards,<br>
</p>
<pre class="moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div class="moz-cite-prefix">On 26/02/2018 12:18, Lucas Michel
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CA+J-Xe1sF2zwuh9yj2Nr4oJZJFian4Tt_uQ5hrucvfTHhq61Yg@mail.gmail.com">
<div dir="ltr"><br>
<div class="gmail_quote">
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<div>
<div>
<div><br>
</div>
I am working on the annotation of some variants on
Plasmodium Falciparum with VEP. Since there is no
reference for it in the ensemble page (or I haven't
found it) I am using a custom GFF and fasta file but
i can not get it to work properly.<br>
<br>
</div>
<div>VEP version:<br>
Versions:<br>
ensembl : 91.18ee742<br>
ensembl-funcgen : 91.4681d69<br>
ensembl-io : 91.923d668<br>
ensembl-variation : 91.c78d8b4<br>
ensembl-vep : 91.3<br>
<br>
</div>
<div><br>
</div>
<div><br>
</div>
Example fragments:<br>
<br>
</div>
VCF file:<br>
<br>
CHROM POS ID REF ALT QUAL FILTER
INFO FORMAT 1.2B_sample 10G_sample
A7K9_sample C2_sample E5K9_sample<br>
Pf3D7_01_v3 12 . A C 371.78 .
AC=5;AF=0.500;AN=10;<wbr>BaseQRankSum=-2.571;DP=166;<wbr>Dels=0.00;ExcessHet=11.9728;<wbr>FS=0.000;HaplotypeScore=13.<wbr>0379;MLEAC=5;MLEAF=0.500;MQ=<wbr>12.68;MQ0=0;MQRankSum=-5.041;<wbr>QD=2.24;ReadPosRankSum=0.232;<wbr>SOR=2.263
GT:AD:DP:GQ:PL 0/1:19,5:24:16:16,0,280
0/1:16,11:27:90:90,0,187 0/1:20,10:30:63:63,0,248
0/1:39,18:57:99:137,0,486 0/1:16,12:28:99:100,0,193<br>
Pf3D7_01_v3 30 . A G 39.92 .
AC=3;AF=0.300;AN=10;<wbr>BaseQRankSum=-7.495;DP=591;<wbr>Dels=0.00;ExcessHet=4.7712;FS=<wbr>0.000;HaplotypeScore=76.2682;<wbr>MLEAC=3;MLEAF=0.300;MQ=12.22;<wbr>MQ0=0;MQRankSum=-4.844;QD=0.<wbr>13;ReadPosRankSum=-1.706;SOR=<wbr>0.405
GT:AD:DP:GQ:PL 0/1:56,13:69:25:25,0,749
0/0:74,14:91:7:0,7,948 0/1:89,24:114:33:33,0,1035
0/0:167,27:197:94:0,94,2087
0/1:93,24:119:18:18,0,1089<br>
Pf3D7_01_v3 37 . G A 10.87 .
AC=2;AF=0.200;AN=10;<wbr>BaseQRankSum=7.016;DP=745;<wbr>Dels=0.03;ExcessHet=3.5218;FS=<wbr>0.000;HaplotypeScore=95.8754;<wbr>MLEAC=2;MLEAF=0.200;MQ=12.26;<wbr>MQ0=0;MQRankSum=-4.419;QD=0.<wbr>03;ReadPosRankSum=1.936;SOR=0.<wbr>962
GT:AD:DP:GQ:PL 0/0:76,10:87:72:0,72,1134
0/0:102,8:111:99:0,151,1577
0/0:110,24:138:89:0,89,1381
0/1:191,50:243:39:39,0,2375 0/1:118,25:146:5:5,0,1533<br>
Pf3D7_01_v3 58 . A G 162.69 .
AC=1;AF=0.100;AN=10;<wbr>BaseQRankSum=-7.121;DP=928;<wbr>Dels=0.01;ExcessHet=3.0103;FS=<wbr>0.000;HaplotypeScore=147.7849;<wbr>MLEAC=1;MLEAF=0.100;MQ=12.57;<wbr>MQ0=0;MQRankSum=-5.615;QD=0.<wbr>68;ReadPosRankSum=0.938;SOR=0.<wbr>445
GT:AD:DP:GQ:PL 0/0:102,11:114:99:0,115,1407 <wbr>
0/0:141,17:159:99:0,160,1896 <wbr>
0/0:162,32:198:66:0,66,1942
0/1:185,56:247:99:195,0,1990 <wbr>
0/0:170,30:201:51:0,51,2099<br>
Pf3D7_01_v3 72 . G A 447.03 .
AC=3;AF=0.300;AN=10;<wbr>BaseQRankSum=7.927;DP=995;<wbr>Dels=0.03;ExcessHet=4.7712;FS=<wbr>0.000;HaplotypeScore=152.4765;<wbr>MLEAC=3;MLEAF=0.300;MQ=12.70;<wbr>MQ0=0;MQRankSum=-5.905;QD=0.<wbr>67;ReadPosRankSum=4.279;SOR=1.<wbr>157
GT:AD:DP:GQ:PL 0/0:112,15:129:99:0,121,1642 <wbr>
0/0:144,21:168:99:0,155,2064 <wbr>
0/1:168,42:210:17:17,0,2079
0/1:186,53:243:99:107,0,2331 <wbr>
0/1:158,60:219:99:360,0,1938<br>
<br>
</div>
GFF file:<br>
<br>
Pf3D7_01_v3 EuPathDB gene 29510 37126 .
+ . ID=PF3D7_0100100;description=<wbr>erythrocyte
membrane protein 1%2C PfEMP1;biotype=protein_coding<br>
Pf3D7_01_v3 EuPathDB exon 29510 34762 .
+ . ID=exon_PF3D7_0100100-E1;<wbr>Parent=PF3D7_0100100.1;<wbr>biotype=protein_coding<br>
Pf3D7_01_v3 EuPathDB CDS 29510 34762 .
+ 0 ID=PF3D7_0100100.1-p1-CDS1;<wbr>Parent=PF3D7_0100100.1;<wbr>protein_source_id=PF3D7_<wbr>0100100.1-p1;biotype=protein_<wbr>coding<br>
Pf3D7_01_v3 EuPathDB mRNA 29510 37126 .
+ . ID=PF3D7_0100100.1;Parent=<wbr>PF3D7_0100100;Ontology_term=<wbr>GO:0050839,GO:0004872,GO:<wbr>0020002,GO:0020030,GO:0016021,<wbr>GO:0020033,GO:0020035,GO:<wbr>0020013,GO:0009405,GO:0016337;<wbr>description=erythrocyte
membrane protein 1%2C PfEMP1;biotype=protein_coding<br>
Pf3D7_01_v3 EuPathDB CDS 35888 37126 .
+ 0 ID=PF3D7_0100100.1-p1-CDS2;<wbr>Parent=PF3D7_0100100.1;<wbr>protein_source_id=PF3D7_<wbr>0100100.1-p1;biotype=protein_<wbr>coding<br>
Pf3D7_01_v3 EuPathDB exon 35888 37126 .
+ . ID=exon_PF3D7_0100100-E2;<wbr>Parent=PF3D7_0100100.1;<wbr>biotype=protein_coding<br>
Pf3D7_01_v3 EuPathDB gene 38982 40207 .
- . ID=PF3D7_0100200;description=<wbr>rifin;biotype=protein_coding<br>
Pf3D7_01_v3 EuPathDB mRNA 38982 40207 .
- . ID=PF3D7_0100200.1;Parent=<wbr>PF3D7_0100200;Ontology_term=<wbr>GO:0020036,GO:0020002,GO:<wbr>0020003,GO:0020033,GO:0020035,<wbr>GO:0020013;description=rifin;<wbr>biotype=protein_coding<br>
Pf3D7_01_v3 EuPathDB exon 38982 39923 .
- . ID=exon_PF3D7_0100200-E2;<wbr>Parent=PF3D7_0100200.1;<wbr>biotype=protein_coding<br>
Pf3D7_01_v3 EuPathDB CDS 38982 39923 .
- 1 ID=PF3D7_0100200.1-p1-CDS2;<wbr>Parent=PF3D7_0100200.1;<wbr>protein_source_id=PF3D7_<wbr>0100200.1-p1;biotype=protein_<wbr>coding<br>
Pf3D7_01_v3 EuPathDB exon 40154 40207 .
- . ID=exon_PF3D7_0100200-E1;<wbr>Parent=PF3D7_0100200.1;<wbr>biotype=protein_coding<br>
Pf3D7_01_v3 EuPathDB CDS 40154 40207 .
- 0 ID=PF3D7_0100200.1-p1-CDS1;<wbr>Parent=PF3D7_0100200.1;<wbr>protein_source_id=PF3D7_<wbr>0100200.1-p1;biotype=protein_<wbr>coding<br>
Pf3D7_01_v3 EuPathDB mRNA 42367 46507 .
- . ID=PF3D7_0100300.1;Parent=<wbr>PF3D7_0100300;Ontology_term=<wbr>GO:0004872,GO:0016021,GO:<wbr>0009405;description=<wbr>erythrocyte
membrane protein 1%2C PfEMP1;biotype=protein_coding<br>
<br>
</div>
<div>FASTA file:<br>
<br>
>Pf3D7_01_v3 | organism=Plasmodium_<wbr>falciparum_3D7
| version=2015-06-18 | length=640851 | SO=chromosome<br>
TGAACCCTAAAACCTAAACCCTAAACCCTA<wbr>AACCCTGAACCCTAAACCCTGAACCCTAAA<br>
CCCTAAACCCTGAACCCTAAACCCTAAACC<wbr>CTGAACCCTAAACCCTGAAACCTAAACCCT<br>
GAACCCTAAACCCTGAACCCTGAACCCTAA<wbr>CCCTAAACCCTAAACCTAAAACCCTGAACC<br>
CTAAACCCTGAACCCTGAACCCTAAACCCT<wbr>GAACCCTAAACCCTAAACCCTGAACCCTAA<br>
ACCCTGAACCCTAAACCCTAAACCCTGAAC<wbr>CCTGAACCCTAAA...<br>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<div><br>
-- <br>
<br>
</div>
<div>I use VEP with the following command:<br>
<br>
vep -i All_SNP.vcf -gff custom.gff.gz -fasta
ref.fasta.gz -o anofile.csv --force_overwrite<br>
<br>
</div>
<div>And I consisteltly get the following error:<br>
<br>
WARNING: Parent entries with the following IDs
were not found or skipped due to invalid
types: PF3D7_0108400.1,PF3D7_0108400.<wbr>2,
PF3D7_0105400.1,PF3D7_0105400.<wbr>2<br>
WARNING: Parent entries with the following IDs
were not found or skipped due to invalid
types: PF3D7_0205700.2,PF3D7_0205700.<wbr>1,
PF3D7_0216700.1,PF3D7_0216700.<wbr>2,
PF3D7_0210100.1,PF3D7_0210100.<wbr>2,
PF3D7_0208700.1,PF3D7_0208700.<wbr>2,
PF3D7_0219400.2,PF3D7_0219400.<wbr>1,
PF3D7_0206900.1,PF3D7_0206900.<wbr>2,
PF3D7_0202600.1,PF3D7_0202600.<wbr>2<br>
Can't use an undefined value as an ARRAY
reference at /home/lucas/Programs/ensembl-<wbr>vep/Bio/EnsEMBL/Transcript.pm
line 1617, <__ANONIO__> line 9772.<br>
<br>
</div>
<div>I added the biotype argument manually on
the gff since i thought the problem might lie
thre but I have had no success.<br>
<br>
</div>
<div>Any help would be much appreciated.<br>
<br>
</div>
<div>Thank you very much,<br>
<br>
</div>
<div>Lucas<br>
</div>
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