For demultiplexing, the VCF file must contain information on all the multiplexed patient samples, i.e. if three samples are multiplexed, the VCF file must contain germline SNVs for all three (it is not possible to provide variants for two, and then deduce the identity of the third patient). Information for all three patients should be defined in a single VCF file as samples; individual patient files are not supported.
Does the VCF need to contain the germline SNV information for all multiplexed samples?
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