Question: How can I pick up SNPs and other mutations in the transcripts assembled by the
cellranger vdj pipeline?
Answer: Our assay outputs reads that span the full-length V(D)J transcript (TRA/TRB and IGH/IGL chains). The key to capturing SNPs and other mutations is de novo assembly of the TRA/TRB and IGH/IGL chains in the V(D)J pipeline. Since our transcript assembly does not rely on alignment to a reference of known V(D)J genes, it does not discard any (SNPs or larger) mutations during assembly.
The image below shows contigs assembled for the 10x Genomics NSCLC T cell dataset. Transcripts with a 6 bp deletion and an A>G mutation in the CDR3 region are aligned against the reference gene segments.