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jeizenga avatar jeizenga commented on June 16, 2024
  1. As far as I can tell, there is only one graph involved here. What do you mean by "merging graphs"?
  2. If you have a PCR step in your library prep, any standard duplicate removal should work for the BAM output. MarkDuplicates is fine.

from vg.

dbrami avatar dbrami commented on June 16, 2024

Thanks for response.

  1. If I have technical replicates and wish to add more depth before variant calling, I would want to combine the aligned BAM files. Iā€™m asking if there are any accuracy gains by merging graphs from technical replicates versus merging BAMs after conversion of graph to BAM.
  2. Yes - thanks for confirming.

from vg.

jeizenga avatar jeizenga commented on June 16, 2024

It sounds like you are actually describing merging the reads before mapping. Is that correct? There is no second graph to be merged here. If I'm correct that you're referring to reads, then it shouldn't matter much. There might be a very small improvement in accuracy if you map the replicates separately and then combine the BAMs, because that will allow each replicate to estimate its own fragment length distribution during read mapping. I would expect the difference to be tiny though.

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