vcftobedpe complains about no END field in LUMPY BNDs.

[jasonbhn]

Hi
In version 0.5.1, I did
svtools vcftobedpe -i gtex.lumpy.gs.melt.high_conf_MAF0.01.vcf -o gtex.lumpy.gs.melt.high_conf_MAF0.01.bedpe
to convert vcf to bedpe files however the error:
ValueError: END entry in VCF required for conversion to BEDPE.
But looking at some other issues there seems to be no complaint when there's no END in BNDs?

Thank you

[anoronh4]

i also encountered this error with 0.5.1, and as a temporary workaround i just filtered out calls with no END. but this is not ideal and it might be necessary to fix or annotate with END info. i don't know too much about SV vcf formatting so i'd be interesting in hearing back from the authors of this repo. did you try other versions of svtools?