biostudies-literatureHaller TEstonian GovernmentNIDDK NIH HHSEstonian Center of Genomics/Roadmap IIEU H2020 grant ePerMedUS National Institute of HealthEU H2020 grantEuropean Regional Development Fund22https://www.ebi.ac.uk/biostudies/studies/S-EPMC6330393biostudies-literatureUnknown20(1)<h4>Background</h4>Selection of interesting regions from genome wide association studies (GWAS) is typically performed by eyeballing of Manhattan Plots. This is no longer possible with thousands of different phenotypes. There is a need for tools that can automatically detect genomic regions that correspond to what the experienced researcher perceives as peaks worthwhile of further study.<h4>Results</h4>We developed Manhattan Harvester, a tool designed for "peak extraction" from GWAS summary files and computation of parameters characterizing various aspects of individual peaks. We present the algorithms used and a model for creating a general quality score that evaluates peaks similarly to that of a human researcher. Our tool Cropper utilizes a graphical interface for inspecting, cropping aBMC bioinformaticsManhattan Harvester and Cropper: a system for GWAS peak detection.PMC63303932014-2020.4.01.15-0012692145IUT20-60R01DK0757872014-2020.4.01.16-0125R01 DK075787633589Metspalu AHaller TTasa TfalseManhattan Harvester and Cropper: a system for GWAS peak detection.<h4>Background</h4>Selection of interesting regions from genome wide association studies (GWAS) is typically performed by eyeballing of Manhattan Plots. This is no longer possible with thousands of different phenotypes. There is a need for tools that can automatically detect genomic regions that correspond to what the experienced researcher perceives as peaks worthwhile of further study.<h4>Results</h4>We developed Manhattan Harvester, a tool designed for "peak extraction" from GWAS summary files and computation of parameters characterizing various aspects of individual peaks. We present the algorithms used and a model for creating a general quality score that evaluates peaks similarly to that of a human researcher. Our tool Cropper utilizes a graphical interface for inspecting, cropping a2019-01-01T00:00:00Z2019 Jan2025-04-25T17:31:29.377Z2019-03-26T22:37:54ZS-EPMC63303933063490110.1186/s12859-019-2600-4