Question: How can we pick up SNPs and other mutations in the transcripts assembled by the cellranger vdj pipeline
Answer: For V(D)J, our assay is designed such that we get reads that span the full length of the transcripts (TRA/TRB and IGH/IGL chains). This is made possible by the fragmentation step in the assay workflow.
The key to capturing SNPs and other mutations is that we do denovo assembly of the TRA/TRB and IGH/IGL chains in V(D)J pipeline. Therefore the transcript sequences that we assemble are not based on alignment to a reference of known V(D)J genes.
If for example were were following an alignment to known V(D)J gene segments based approach, the reads carrying larger mutations might not have aligned well to any of the genes in the reference and we might have lost them in the analysis.
The denovo assembly method allows us to capture the SNPs and other mutations in the transcripts. For example below screenshot shows the alignment of the contigs we assembled for our NSCLC T cell dataset. It shows that we assembled transcripts with 6 bp deletion and A>G mutation in the CDR3 region as compared to the reference gene segments.
