PT  - JOURNAL ARTICLE
AU  - Brent S. Pedersen
AU  - Aaron R. Quinlan
TI  - Who’s who? Detecting and resolving sample anomalies in human DNA sequencing studies with <em>peddy</em>
AID  - 10.1101/074385
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 074385
4099  - http://biorxiv.org/content/early/2016/09/09/074385.short
4100  - http://biorxiv.org/content/early/2016/09/09/074385.full
AB  - The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from the cohort are mislabelled, swapped, contaminated, or include unintended individuals. Unfortunately, the potential for such errors is significant since DNA samples are often manipulated by several protocols, labs or scientists in the process of sequencing. We have developed peddy to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from each individual’s genotypes. Peddy predicts a sample’s ancestry using a machine learning model trained on individuals of diverse ancestries from the 1000 Genomes Project reference panel. Peddy’s speed, text reports and web interface facilitate both automated and visual detection of sample swaps, poor sequencing quality and other indicators of sample problems that, were they left undetected, would inhibit discovery.Software Availability https://github.com/brentp/peddyDemonstration (Chrome suggested) http://home.chpc.utah.edu/∼u6000771//plots/ceph1463.html