Cell Ranger2.0, printed on 11/14/2024
The cellranger vdj pipeline will generate .vloupe files for Single Cell
V(D)J experiments. A .vloupe file will be found in the outs folder of
a completed Cell Ranger vdj run.
The .vloupe file contains information about clonotypes and contig/consensus alignments,
but does not contain the contig BAM file necessary to validate read support with the integrated IGV.js viewer.
If the all_contig.bam file is not present in the same folder as the .vloupe file, you will be prompted
to enter either its location on a filesystem, or a web address where the file can be found. If you are
interested in validating read support, it may be worth it to keep the .vloupe and all_contig.bam files
together, though the all_contig.bam file can grow very large.
You will still need to consult the Cell Ranger run summary file to view quality control data and other metadata about a particular run; this is not yet available in Loupe V(D)J Browser.