What are productive contigs?

Question: What does the Productive column mean in the contig_annotations.csv file generated by cellranger vdj? 

Answer: The Productive column in the all_contig_annotations.csv (or filtered_contig_annotations.csv) identifies contigs that are predicted to generate functional proteins. For a contig to be marked as productive it must:

1.  Be V-J spanning with a start codon in the leader region.
2.  Have a detectable CDR3 region in frame with the start codon.
3.  Be free of stop codons in the V-J spanning region.