vcftobedpe fails for certain MANTA calls

[axelgschwind]

Hello,

we are using svtools to creating bedpe files that originate both from MANTA and Delly.

In some cases, MANTA generates a structural variant call that looks like this:

chrX 88459900 MantaBND:196720:0:1:8:0:0:0 A ]CHRY:6402446]A . MaxDepth IMPRECISE;SVTYPE=BND;CIPOS=-153,153;MATEID=MantaBND:196720:0:1:8:0:0:1;BND_DEPTH=119;MATE_BND_DEPTH=40 PR 0,0

However, the original MANTA file does not include the Mate read with the corresponding ID. Having such a Manta vcf, svtools crashes with the error message:

Warning: missing secondary multiline variant at ID:MantaBND:196720:0:1:8:0:0:0

I am not sure whether this is a bug. However, is it may possible to make svtools print a warning only instead of stopping the whole script?

Greetings,

Axel