Closed uceleste closed 5 years ago
Both the pipelines you suggest are not really supported, or tested, although I expect the pipeline with the sort is doing the correct thing. As a check I would use the supported workflow pbalign, followed by ipdSummary. pbalign sorts and indexes the ouput bam, so it should be equivalent to your pipeline 1, although it's possible that the default alignment parameters are also different. https://github.com/PacificBiosciences/pbalign
Thank you for your kind explanation.
Hi All,
I tried ipdSummary on two parallel pipelines using the same reads and reference. The only difference is that in one case the alignment file in bam format was sorted and in the other case no. I obtained two different output with some shared information.
What is the correct way to run the process? Is it always better to do the sorting of the bam alignment?
Here my command lines and a semplified example of both output:
Pipeline 1
Pipeline 2
Thank you