What are the major updates in Cell Ranger v7.1 that impacts V(D)J data?

Question:

I am currently using Cell Ranger v7.0. What are the changes in Cell Ranger v7.1 that influences the V(D)J results?

Answer:

The latest Cell Ranger v7.1 release, available from our downloads page, has significant improvements and bug fixes. In this article, we discuss the V(D)J algorithm changes in v7.1, that show improved metrics in VDJ data analysis.

V(D)J algorithm updates: 

In v7.1, the V(D)J+GEX analysis pipeline has improved filter criteria that may help gain more VDJ cells in the presence of Gene Expression data. These changes in the V(D)J filters are applicable only in the presence of Gene Expression (GEX) data. For instance, the Cell Ranger version 7.1.0 algorithm does not filter clonotypes having identical chains in the presence of GEX data. Also we have turned on a CDR3 length filter that checks for the same length before joining the exact sub clonotypes into clonotypes. 

All these changes result in a slight increase in the number of cells called in the VDJ data. This in-turn gives rise to few other metrics in the web_summary.html.  In the below table, we list out the key metric changes that we noticed while testing Cell Ranger v7.0.1 multi and v7.1.0 multi on our 10k human PBMC GEX+TCR+BCR public dataset.

Due to these minor changes in results, if there are old datasets that were analyzed with Cell Ranger v7.0.1 or earlier, it is not required to re-do using the latest Cell Ranger v7.1.0. For more information on whether to re-run data analysis using the latest version, please see this article: My samples are analyzed with Cell Ranger 7.0. Should I reanalyze them using the latest Cell Ranger 7.1?

Note: The impact of updates in v7.1 on Single Cell Gene Expression products is discussed in the article here: What are the cell calling updates in Cell Ranger 7.1 and its impact on Single Cell Gene Expression data?. 

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