vcftobedpe complains about no END field in LUMPY BNDs.

hall-lab / svtools

Tools for processing and analyzing structural variants.

MIT License

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vcftobedpe complains about no END field in LUMPY BNDs. #307

Open jasonbhn opened 3 years ago

jasonbhn commented 3 years ago

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 commented 3 years ago

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?