pLoF Metrics by Gene TSV columns

Constraint
1

Hello,

I’m looking for documentation on the columns in the “pLoF Metrics by Gene TSV” file, v2 Downloads (https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz). On the website, I found the following reference:

“For information on constraint, see The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020). Descriptions of the fields in these files can be found in the Supplementary Dataset 11 section on pages 74-77 of the Supplementary Information.”

However, I couldn’t locate pages 74-77 in Supplementary Dataset 11. From what I’ve downloaded, it seems that Dataset 11 is the Gene constraint file itself, not the documentation.

Could you please help clarify what I might be missing?

Thank you!

2

Hello,

A description of the fields can be found in the Supplementary Information (rather than the Supplementary Dataset).

Regards,
Kristen

3

Thank you!

I came across the following note in the Supplementary Information:

“Note that this file contains all transcripts: for gene-based analyses, the file should be filtered to canonical transcripts (canonical == true), and LOEUF decile bin (oe_lof_upper_bin) recomputed for each gene.”

Could you please clarify how I can filter the file to include only the canonical transcripts? I assumed there would be a specific filter column for this, but I couldn’t find it.

Thank you

4

Hello,

That note refers to the “pLoF Metrics by Transcript TSV” download, which has “canonical” at the third column.

Regards,
Kristen