Error during combine of Manta SV sites about bayestyper

[jonassibbesen]

This seems to be an issue with parsing the VCF file. I do not expect it to be the prior since we have used it many times before without any problems. One possible issue that could raise this error is if not all lines in your vcf has the same number of columns or if the file does not end with a newline character. If this is not the issue would it be possible for you to share the file with me?

[jjfarrell]

@jonassibbesen I have found the one variant that is triggering this error and created a vcf that I can share. let me know how to get it to you.

[iprada]

Hi @jjfarrell. I have run into a similar issue. Could you share the source of the error so that I handle it?
Thanks!

[jjfarrell]

@lprada and @jonassibbesen I eventually found the source of the error. I typically use bgzip to compress vcf files. That allows the file to be indexed. For the candidate vcf input to bayestyper, it must be gzipped. Once I made this change, I never got the error again. There must be a slight difference in the compression that bayestyper can not handle. It would be nice to have bayestyper read bgzip files to allow indexing with tabix.

[jonassibbesen]

Glad to hear you found the issue. Yeah, it is a known issue that bgzip does does not work with the boost compression library that we use. It should be possible to support bgzip using htslib. However, I unfortunately do not have time to work on this in the near future.