ERROR in battenberg for XY samples only

[pumpkinpark97]

Dear authors, @NMNS93 @elarosecadieux ,

I encountered an error when executing CAMDAC::pipeline with WGBS bam file.

The strange thing is that the Battenberg process only completes successfully for the BAM file of male patients, allowing for purity calling.

However, when the BAM file of a female patient is used as input, the Battenberg process halts after haplotyping up to chromosome 22.

The last output message is as follows: 2024-08-30 17:12:33.096258 INFO::Battenberg RUN HAPLO COMPLETE for 22

The error message is as follows:

Error in `[<-`(`*tmp*`, BAFs <= minBaf, 1, value = 1) : 
  (subscript) logical subscript too long
Calls: <Anonymous> ... withCallingHandlers -> <Anonymous> -> generate.impute.input.wgs
In addition: Warning message:
Unknown argument 'on' has been passed. 
Execution halted

Is there any way to fix this problem OR call purity without sex chromosome?

Any help is appreciated ! thanks

[elarosecadieux]

Hi, @NMNS93 is the point person for CAMDAC WGBS. He is currently on holiday with little to no access to the internet. In the meantime, I will reach out to the Battenberg authors for you and see if I can implement a quick patch for this issue! Thanks, Lili

[NMNS93]

Thanks for raising this issue! We're currently looking into it. Please note that the WGBS tool is still in development but we expect this to be resolved with an official release in the coming months.