Comments (2)
Hi @Crispy13 ,
We use the "reference" and "reads" from the same sample to reduce this confusion. For example, when DeepConsensus was first trained, we used HG002 assembly (or reference) as the truth for the reads. There are haploid samples like CHM13 that reduce this issue further. So, usually when we use the assembly of the sample sample we don't expect all of the variation to be present in the assembly.
I hope this helps. You can read more about genome assembly here
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Thank you for replying
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