Dandelion for TCR gamma/delta reannotation

In Cell Ranger 3.1.0, the VDJ algorithm was changed to favour TCR alpha/beta annotation. Since then, calling gamma/delta chains has become challenging, and 10X support recommends using Cell Ranger 3.0.2 when working with gamma/delta-rich libraries.

However, the contigs themselves are still accurately reconstructed, just not annotated correctly. It may be desirable to use a newer Cell Ranger version for access to some previously unavailable run options, like specifying custom enrichment primers. In those cases, the contigs can be reannotated via dandelion to yield functional output.

Just follow standard protocol for preparing and running the preprocessing. The parameterisation recommendation is applicable here as well:

singularity run -B $PWD /path/to/sc-dandelion_latest.sif dandelion-preprocess \
     --chain TR \
     --file_prefix all \
     --filter_to_high_confidence