[ensembl-dev] variant effect predictor duplicate output lines

Will McLaren wm2 at ebi.ac.uk
Tue Aug 30 09:50:14 BST 2011


Thanks for spotting this Michael, this has been fixed on branch 63.

Will

On 28 August 2011 21:53, Michael Yourshaw <myourshaw at ucla.edu> wrote:
> I’m observing duplicate output lines with VEP under some cases. My test case
> is a VCF file with 32 variants involving 13 chromosomes. My command line is:
> --buffer_size 5000 -input_file /Volumes/storage/vw/snp1_test.vcf --format
> vcf -output_file /Volumes/storage/vw/snp1_test.vcf.vep --force_overwrite
> --terms SO --sift=b --polyphen=b --condel=b --regulatory --hgnc --hgvs
> --protein --gene --check_ref --host localhost —no_progress
> It looks like in whole_genome_fetch, at line
> 1437 &print_consequences($config, \@finished_vfs)is not clearing
> out @finished_vfs after calling print_consequences so the first time through
> it prints chr X, the second time chr X and chr 1, then X, 1, 2, etc.
> adding an undef @finished_vfs; after this line seems to fix the issue.
>
>>
> Michael Yourshaw
>
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
> 695 Charles E Young Drive S
> Gonda 5554
>
> Los Angeles CA 90095-8348 USA
>
> myourshaw at ucla.edu
>
> 970.691.8299
>
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