[ensembl-dev] variant_effect_predictor.pl: warning/error using SNPs on chrs with mixed character/numeric vals

[Janet Young]

Hi there,

I think I've found a very minor issue with variant_effect_predictor.pl.  As far as I can tell, it's not affecting the output in any major way (might cause sorting issues - not sure). I'm still at the early stages of using the script, so it's also possible I've messed something up.  

Anyway, I'm currently trying the script on some of our drosophila data. If my vcf file has SNPs  from a mix of chromosomes with numeric names (e.g. 4) and character names (e.g. 3RHet), I get a sorting error.   If I split the vcf file so that the chr 4 and chr 3RHet SNPs are in separate files, there's no error.

The output looks OK, I think, but it still seemed worth letting you know about this (I always get a little paranoid that output will be messed up when I see any error - it'd be nice to get it fixed at some point).   Looking at VEP.pm I think I can see why that error comes up.

I've attached a small example input file. Here's the error:
Argument "3RHet" isn't numeric in numeric comparison (<=>) at /home/jayoung/malik_lab_shared/perl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1235, <GEN0> line 6.

and here's the full command and output:

variant_effect_predictor.pl --cache --dir /home/jayoung/malik_lab/public_databases/Ensembl/VariantEffectPredictorCache --species drosophila_melanogaster --input_file testCombined3RHetand4small.vcf -o testCombined3RHetand4small.vcf.annotLocal

2014-02-06 10:39:31 - Read existing cache info
2014-02-06 10:39:35 - Starting...
2014-02-06 10:39:35 - Detected format of input file as vcf
2014-02-06 10:39:35 - Read 6 variants into buffer
Argument "3RHet" isn't numeric in numeric comparison (<=>) at /home/jayoung/malik_lab_shared/perl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1235, <GEN0> line 6.
2014-02-06 10:39:35 - Reading transcript data from cache and/or database
[================================================================================================]  [ 100% ]
2014-02-06 10:39:35 - Retrieved 253 transcripts (0 mem, 253 cached, 0 DB, 0 duplicates)
2014-02-06 10:39:35 - Analyzing chromosome 3RHet
2014-02-06 10:39:35 - Analyzing variants
[================================================================================================]  [ 100% ]
2014-02-06 10:39:35 - Calculating consequences
[================================================================================================]  [ 100% ]
2014-02-06 10:39:35 - Analyzing chromosome 4
2014-02-06 10:39:35 - Analyzing variants
[================================================================================================]  [ 100% ]
2014-02-06 10:39:35 - Calculating consequences
[================================================================================================]  [ 100% ]
2014-02-06 10:39:35 - Processed 6 total variants (6 vars/sec, 6 vars/sec total)
2014-02-06 10:39:35 - Wrote stats summary to testCombined3RHetand4small.vcf.annotLocal_summary.html
2014-02-06 10:39:35 - Finished!

I have a current version of variant_effect_predictor.pl (74), and should have a current version of the ensembl perl API (v74, downloaded Jan 24).   (as for another question I sent yesterday, here's a disclaimer:  I AM using a more recent version of Bioperl than is recommended in the installation instructions, I'm afraid (http://uswest.ensembl.org/info/docs/api/api_cvs.html) - I needed that for other projects, and have not put any time into figuring out how to have old and new Bioperls installed simultaneously, and how to point Ensembl towards the older one.    I don't think that's causing the issue here, though)

thanks again,

Janet Young

------------------------------------------------------------------- 

Dr. Janet Young 

Malik lab
http://research.fhcrc.org/malik/en.html

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., A2-025, 
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 4512
email: jayoung  ...at...  fhcrc.org

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