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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Confuse in discordant paired-end or paired-end ? #340

Open PhanNgan opened 4 years ago

PhanNgan commented 4 years ago

Hello, I see your example workflow, I am confusing in some points below:

  1. First, you run histo for "sample.bam" and you have "sample.lib1.histo", then for different Lumpy run you use "sample.lib1.histo" and "sample.pe.histo". Do we also run histo for paired-end read?
  2. Second, several bam file with different name for discordant, paired-end, splitters sample.discordants.bam sample.pe.sort.bam sample.splitters.bam sample.sr.sort.bam Do "sample.discordants.bam" equal to "sample.pe.sort.bam" ? and "sample.splitters.bam" equal to "sample.sr.sort.bam"?
  3. For Lumpy traditional, there is no combination between "sample.bam", "sample.discordants.bam" and "sample.splitters.bam" Could you please help me to better understand your workflow? Thank you very much