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
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
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