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

[Allison Regier]

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

____
This email message is a private communication. The information transmitted, including attachments, is intended only for the person or entity to which it is addressed and may contain confidential, privileged, and/or proprietary material. Any review, duplication, retransmission, distribution, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is unauthorized by the sender and is prohibited. If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20141210/901007c2/attachment.html>