Missing SVTYPE info in base vcf

[valeandri]

Hi,

I am using witty.er on GIAB SV dataset and the tool gives me this exception:

Unhandled Exception: System.IO.InvalidDataException: Following variant does not have SVTYPE info key:
chr1    964542  HG3_Ill_SVrefine2DISCOVARDovetail_2 GGCTGCGGGGAGGGGGGCGCGGGTCCGCAGTGGGGCTGTGGGAGGGGTCCGCGCGTCCGCAGTGGGGATGT G   20  PASS    .   GT:GTcons1:PB_GT:PB_REF:PB_ALT:PBHP_GT:PB_REF_HP1:PB_ALT_HP1:PB_REF_HP2:PB_ALT_HP2:TenX_GT:TenX_REF_HP1:TenX_ALT_HP1:TenX_REF_HP2:TenX_ALT_HP2:ILL250bp_GT:ILL250bp_REF:ILL250bp_ALT:ILLMP_GT:ILLMP_REF:ILLMP_ALT:BNG_LEN_DEL:BNG_LEN_INS:nabsys_svm    1/1:1/1:1/1:3:52:1/1:2:12:0:9:./.:1:0:5:0:0/0:8:0:./.:.:.:.:.:.
   at Ilmn.Das.Core.Tries.Extensions.Try.GetOrThrow[TSource](ITry`1 source)
   at Wittyer.Program.LaunchWittyerMain(String[] args) in /src/Wittyer/Program.cs:line 49
   at Wittyer.Program.Main(String[] args) in /src/Wittyer/Program.cs:line 22

I am using witty.er 0.3.5.1 built as docker image.

Thanks, Valentina

[Kentalot]

please use this branch. I will be deploying a few new versions soon though as well. But for now, this will get you past it: https://github.com/Illumina/witty.er/tree/Kentalot-patch-1

[valeandri]

Thanks @Kentalot.

I build the docker image from the branch suggested but it fails with this error:

usr/share/dotnet/sdk/5.0.408/Sdks/Microsoft.NET.Sdk/targets/Microsoft.NET.EolTargetFrameworks.targets(28,5): warning NETSDK1138: The target framework 'netcoreapp2.0' is out of support and will not receive security updates in the future. Please refer to https://aka.ms/dotnet-core-support for more information about the support policy. [/src/Ilmn.Das.App.Wittyer/Ilmn.Das.App.Wittyer.csproj]
16.86 /src/Ilmn.Das.App.Wittyer/Vcf/Variants/WittyerType.cs(158,17): error CS0177: The out parameter 'svType' must be assigned to before control leaves the current method [/src/Ilmn.Das.App.Wittyer/Ilmn.Das.App.Wittyer.csproj]

Do I have to modify something to get it work?

[Kentalot]

I have pushed a major update to master, please use that branch instead now. Dockerfile has changed. There's a bunch of major new features but the README is still in the process of being updated but the normal behavior is still there as well, so you should be able to use it as is. You can run --help to see the new options.

[valeandri]

Thanks @Kentalot, now it is working!

I'll close the issue.

Have a nice day and thanks for the tool.