[ensembl-dev] vep --custom with bed files boundary error

[Will McLaren]

Hi Allison,

Apologies for the delay in getting back to you. This has now been fixed in
v78; please let me know if you would like me to back-patch the fix to any
older releases.

You should be able to get the update by either rerunning INSTALL.pl or
pulling ensembl-variation from git, depending on how you set up the VEP.

Regards

Will McLaren
Ensembl Variation

On 11 December 2014 at 00:52, Allison Regier <aregier at genome.wustl.edu>
wrote:
>
> We seem to be seeing an off-by-one boundary error when using the —custom
> flag annotating a vcf with bed files.
> For example,
> test.bed:
> 1       69428   69429   TEST1
> 1       69429   69438   TEST2
>
> bgzip text.bed
> tabix -p bed test.bed.gz
>
> test vcf:
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
> 1       69427   .       A       T       .       .       .       .
> 1       69428   .       A       T       .       .       .       .
> 1       69429   .       T       G       .       .       .       .
> 1       69430   .       A       T       .       .       .       .
>
> command:
> perl variant_effect_predictor.pl —custom test.bed.gz,CUSTOM,bed,overlap,0
> —species homo_sapiens —input_file test.vcf —format vcf —vcf
>
> test.output.vcf:
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
> 1       69427   .       A       T       .       .
> CSQ=T|ENSG00000186092|ENST00000335137|Transcript|NON_SYNONYMOUS_CODING|337|337|113|I/F|Att/Ttt|||YES|OR4F5|HGNC|||
> .
> 1       69428   .       A       T       .       .
> CSQ=T|ENSG00000186092|ENST00000335137|Transcript|NON_SYNONYMOUS_CODING|338|338|113|Y/F|tAt/tTt|||YES|OR4F5|HGNC|||;
> *CUSTOM=TEST1* .
> 1       69429   .       T       G       .       .
> CSQ=G|ENSG00000186092|ENST00000335137|Transcript|NON_SYNONYMOUS_CODING|339|339|113|F/L|ttT/ttG|||YES|OR4F5|HGNC|tolerated(0.13)|probably_damaging(0.928)|deleterious(0.628);
> *CUSTOM=TEST2,TEST1*  .
> 1       69430   .       A       T       .       .
> CSQ=T|ENSG00000186092|ENST00000335137|Transcript|NON_SYNONYMOUS_CODING|340|340|114|N/Y|Aac/Tac|||YES|OR4F5|HGNC|deleterious(0)|probably_damaging(0.996)|deleterious(0.906);
> *CUSTOM=TEST2* .
>
> VCF should be 1 based and BED should be 0 based : only 69429 should be
> annotated as TEST1, not 69428
> similarly, only 69430 should be annotated as TEST2, not 69429
>
> Any suggestions if we are doing something wrong, or is this a bug?
>
> We were originally running with v74 but the problem still exists in v78.
> thanks,
> Allison Regier
>
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