Ming Tang

Please add this feature, thanks very much!

YES, `vcfanno -nearest 4 -maxdist 100000` works for me. Thanks!

if it is not of too much work, could you please add options to restrict nearest genes upstream or downstream of the breakpoint? it has to do with the strandness...

Please see attachment for the vcf file and below for the bed file. Thanks! ``` chr10 34048641 34061608 - NR_038932 chr15 38226808 38243623 + NM_152453 chr15 37091301 37110707 - NR_027320...

@brentp yes, upstream based on the strand of the BND event. Thanks very much!

Note that some breakpoints (at the start or end of a chromosome) will not have a closest upstream gene.

That's what I think. However, please look at Colby Chiang's comments on my question as well https://github.com/hall-lab/svtools/issues/5 My vcf is from lumpy output. I do think the strandness makes sense...

if you look at this particular example: ``` 8 9174263 5956_1 N N[14:38454918[ 25.35 . SVTYPE=BND;STRANDS=+-:4;CIPOS=-9,8;CIEND=-9,8;CIPOS95=0,0;CIEND95=0,0;MATEID=.... 14 38454918 5956_2 N ]8:9174263]N 25.35 . SVTYPE=BND;STRANDS=-+:4;CIPOS=-9,8;CIEND=-9,8;CIPOS95=0,0;CIEND95=0,0 ``` when converted to bedpe: ```...

1 year later, wondering if it is now implemented or not. Thanks!

sorry, it was a typo. it is 0.20.0. Is this the latest version?