GERP

Overview

GERP identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint (Rejected Substitutions). Nirvana uses GERP++ which is based on a significantly faster and more statistically robust maximum likelihood estimation procedure to compute expected rates of evolution.

Publication

Davydov, Eugene V., et al. "Identifying a high fraction of the human genome to be under selective constraint using GERP++." PLoS computational biology 6.12 e1001025 (2010). https://doi.org/10.1371/journal.pcbi.1001025

Source Files

Example GRCh37

GRCh37 file is a TSV format

chr     position    GERP
1       12177       0.83
1       12178       -0.206
1       12179       -0.492
1       12180       -1.66
1       12181       0.83
1       12182       0.83
1       12183       -0.417
1       12184       0.83

Example GRCh38

GRCh38 file is a lift-over BED format

chr     pos_start   pos_end     GERP
1       12646       12647       0.298
1       12647       12648       2.63
1       12648       12649       1.87
1       12649       12650       0.252
1       12650       12651       -2.06
1       12651       12652       2.61
1       12652       12653       3.97

Parsing

From the CSV file, we are interested in columns:

• chr
• position
• GERP

Known Issues

None

Download URL

GRCh37

http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html

GRCh38

The data is not available for GRCh38 on GERP++ website, and was obtained from https://personal.broadinstitute.org/konradk/loftee_data/GRCh38/

JSON Output

"gerpScore": 1.27

Field	Type	Notes
gerpScore	float	Range: -∞ to +∞