aligning to a multi-reference w/ ambiguities

[stanleyjs]

Hello,

We have create a multi-reference that features a lot of sequence similarity in it (the multi reference is GRCh38 + Clade B, the collection of identified north american HIV variants). We expect some multi-mapping of reads to both GRCh38 loci and Clade B loci. We have determined a set of rules for resolving alignment ambiguities. We would like to run CR on the multi reference, parse the BAM for multi alignments, apply our rules to resolve ambiguities, and then obtain the remaining UMI counts that were previously ambiguous.

Is there a pipeline for this? We are comfortable writing our own BAM parser but not sure how best to mold this into CR's UMI assignment procedure.

[elehnert10x]

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