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<div dir="ltr"><font color="#000000" size="2" face="Tahoma">Hi,</font></div>
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<div dir="ltr"><font face="tahoma">I have been trying to use gtf2vep.pl<a></a> to generate a cache file based on RhesusBase<a></a> (<a href="http://www.rhesusbase.org/">http://www.rhesusbase.org/</a>) gene annotations on the UCSC<a></a> rheMac2<a></a>/Ensembl<a></a> MMUL_1<a></a>
assembly. I downloaded their rb2<a></a> gene predictions as a gtf<a></a> file through their UCSC<a></a> mirror, changed the source column to "protein_coding<a></a>", added "exon_number<a></a>" and the appropriate number in the description field, and sorted
the annotations by chromosome position. The gtf<a></a> file can be downloaded from here:</font></div>
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<div dir="ltr"><a href="https://bigfile.bcm.edu/download.php?claimID=tnwUAesf9rRRH3u5&claimPasscode=B8mm8RNVZG4Ub6Xy&fid=52811&emailAddr=rharris1@bcm.edu">https://bigfile.bcm.edu/download.php?claimID=tnwUAesf9rRRH3u5&claimPasscode=B8mm8RNVZG4Ub6Xy&fid=52811&emailAddr=rharris1@bcm.edu</a></div>
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<div dir="ltr"><font face="tahoma">When I run gtf2vep.pl<a></a> I get this error:</font></div>
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<div dir="ltr"><font face="tahoma">Can't call method "start" on an undefined value at gtf2vep.pl<a></a> line 376.</font></div>
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<div dir="ltr"><font face="tahoma">This error occurs after generating some of the cache files in the .vep<a></a> directory. I tried to run gtf2vep.pl<a></a> using gtf<a></a> files with only a single chromosome and it looks like the error consistently occurs
when trying to generate the 1-1000000 cache file. Oddly, if I just run gtf2vep.pl<a></a> on the annotations from 1-1000000 on a single chromosome I do not get this error.</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">I don't think this is due to chr<a></a> in chromosome names because the fasta<a></a> file I am using has chr<a></a> in the chromosome names.</font></div>
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<div dir="ltr"><font face="tahoma">I would appreciate any help you could give me with this.</font></div>
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<div dir="ltr"><font face="tahoma">Thanks,</font></div>
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<div dir="ltr"><font face="tahoma">Alan</font></div>
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