Closed scwatts closed 2 years ago
@mkirsche Does that sound familiar? We're currently in an accreditation process and this is a potential blocker; I'd love to use Jasmine for this if at all possible. Thank you!
Hi,
Sorry for the late response! Jasmine does not currently support maintaining breakend pairs; it assumes that each variant is represented by a single entry, representing breakend pairs with either CHR2/END INFO fields or the colon-delimited ALT field specified in the VCF file format. I am hoping to update this behavior in the next version of Jasmine, but that is at least a few weeks out. In the meantime, I would recommend merging BND pairs into single entries to avoid this issue.
Best, Melanie
Thanks for the update!
Hi Melanie, I've had some time today to return to this - your suggestion has worked well, thank you!
Hello, thanks for creating and publishing Jasmine!
I've encountered a situation where a breakend variant in one sample does not merge with the identical variant in a second sample but instead merges with the mate/partner e.g.
variant_a
andvariant_b
represent a paired set of beakends, and are present in two VCFs/samples:I have found that Jasmine can produce the resulting merged variants:
I dont think this is intended behaviour. I've created and attached a minimal example to reproduce below.
Minimal example
Expected behaviour
first.vcf
:second.vcf
:input_files.txt
:Merge variants:
Unexpected behaviour
Repeat exactly as above but including the
INFO/DEBUG_1234
field infirst.vcf
to trigger the unexpected behaviour.first.vcf
:second.vcf
:input_files.txt
:Install info
Above was done using Jasmine 1.1.4 on macOS from conda and installed via: