[ensembl-dev] VEP text output sort order

cj5 at sanger.ac.uk cj5 at sanger.ac.uk
Mon Oct 17 16:40:15 BST 2011


Further to this, here's an extract from my log output, looks like a sort
problem with the buffer:

2011-10-03 14:15:54 - Read 20000 variants into buffer
2011-10-03 14:15:54 - Analyzing chromosome 1
2011-10-03 14:15:54 - Reading transcript data from cache and/or database
2011-10-03 14:16:12 - Analyzing variants
2011-10-03 14:18:21 - Analyzing chromosome 2
2011-10-03 14:18:21 - Reading transcript data from cache and/or database
2011-10-03 14:18:40 - Analyzing variants
2011-10-03 14:20:01 - Read 20000 variants into buffer
2011-10-03 14:20:03 - Analyzing chromosome 2
2011-10-03 14:20:03 - Reading transcript data from cache and/or database
2011-10-03 14:20:06 - Analyzing variants
2011-10-03 14:20:23 - Analyzing chromosome 3
2011-10-03 14:20:23 - Reading transcript data from cache and/or database
2011-10-03 14:20:47 - Analyzing variants
2011-10-03 14:22:01 - Analyzing chromosome 4
2011-10-03 14:22:01 - Reading transcript data from cache and/or database
2011-10-03 14:22:19 - Analyzing variants
2011-10-03 14:23:09 - Analyzing chromosome 5
2011-10-03 14:23:09 - Reading transcript data from cache and/or database
2011-10-03 14:23:26 - Analyzing variants
2011-10-03 14:24:19 - Analyzing chromosome 6
2011-10-03 14:24:19 - Reading transcript data from cache and/or database
2011-10-03 14:24:24 - Analyzing variants
2011-10-03 14:25:00 - Read 20000 variants into buffer
2011-10-03 14:25:01 - Analyzing chromosome 10
2011-10-03 14:25:01 - Reading transcript data from cache and/or database
2011-10-03 14:25:02 - Analyzing variants
2011-10-03 14:25:04 - Analyzing chromosome 6
2011-10-03 14:25:04 - Reading transcript data from cache and/or database
2011-10-03 14:25:21 - Analyzing variants
2011-10-03 14:26:11 - Analyzing chromosome 7



Tx
Chris


> Hi,
> I've noticed that the VEP 2.2. text output order is occasionally not in
> genomic order for a small percentage of records. I'm using the hs cache
> for this like so:
>
> variant_effect_predictor.pl -v -i <my 120K record vcf> --sift b --polyphen
> b --condel b --gene --hgnc --format vcf -o <my output file>
> --force_overwrite --cache --dir <my vep_cache>
>
> Output:
> ...
> 6_4998993_C/T   6:4998993   T   ENSG00000124787 ENST00000380051 Transcript
>  SYNONYMOUS_CODING   561 516 172 K   aaG/aaA -   HGNC=RPP40
> 10_93502_C/G    10:93502    G   ENSG00000173876 ENST00000482075 Transcript
>  DOWNSTREAM
> ...
> [several hundred chr10 records then jump back to chr 6]
>
> Is this a know issue?
>
> Thanks
> Chris
>
>
>
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