MiSeq pipeline, per-genome bam vs per chromosome bam & vcf

[swNGS]

Hi,
Am am developing an open-source pipeline for DNA resequencing experiments that will be done on a MiSeq. I waned to take advantage of its own internal pipeline to allow benchmarking of whatever I come up with.

Unfortunately, the defaul behaviour of the MiSeq's pipeline is to output per-chromosome bams and vcfs rather than per-genome files.
For a highly multiplexed run this is quite a problem.

While I could combine the name and vcfs, I was wondering if anyone had come up with a hack to make it do this?
Illumina say that it is not possible to introduce any user-configuration switches at the point of the sample sheet, but this 'funcionality' will be added in future release of MiSeq Reporter.

If anyone has come up with a way to get around this without having to merge these files after the event, then I would be most interested to hear from you

Thanks,

Chris

[GenoMax]

Chris: You can analyze the data from MiSeq off-line with CASAVA. That should get around the problems you mention. It would not be automatic but then you could fire off the two analysis processes (CASAVA and your pipeline) at the same time.

Hi,


If anyone has come up with a way to get around this without having to merge these files after the event, then I would be most interested to hear from you

Thanks,

Chris