National Center for Toxicological Research (NCTR) analysis of WES1, WES2, and WES3

WJ Wendell Jones
BG Binsheng Gong
NN Natalia Novoradovskaya
DL Dan Li
RK Rebecca Kusko
TR Todd A. Richmond
DJ Donald J. Johann, Jr
HB Halil Bisgin
SS Sayed Mohammad Ebrahim Sahraeian
PB Pierre R. Bushel
MP Mehdi Pirooznia
KW Katherine Wilkins
MC Marco Chierici
WB Wenjun Bao
LB Lee Scott Basehore
AL Anne Bergstrom Lucas
DB Daniel Burgess
DB Daniel J. Butler
SC Simon Cawley
CC Chia-Jung Chang
GC Guangchun Chen
TC Tao Chen
YC Yun-Ching Chen
DC Daniel J. Craig
AP Angela del Pozo
JF Jonathan Foox
MF Margherita Francescatto
YF Yutao Fu
CF Cesare Furlanello
KG Kristina Giorda
KG Kira P. Grist
MG Meijian Guan
YH Yingyi Hao
SH Scott Happe
GH Gunjan Hariani
NH Nathan Haseley
JJ Jeff Jasper
GJ Giuseppe Jurman
DK David Philip Kreil
Paweł Łabaj
KL Kevin Lai
JL Jianying Li
QL Quan-Zhen Li
YL Yulong Li
ZL Zhiguang Li
ZL Zhichao Liu
ML Mario Solís López
KM Kelci Miclaus
RM Raymond Miller
VM Vinay K. Mittal
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The NCTR team’s pipelines were applied on WES1, WES2, and WES3 datasets. Reference genomes were downloaded from Illumina iGenomes website for both hg19 and hg38 version. Reads were aligned with BWA-MEM [29] (v0.7.12-r1039) and Bowtie2 [31] (v2.3.2). Duplicate reads were marked using Picard [56] (v2.7.1) MarkDuplicates function. The reads were then local realigned around small insertions and deletions (indels) and base quality scores were recalibrated using GATK [58] (v3.6-0-g89b7209). dbSNP (b150) was supplied to GATK for indel realignment and quality score recalibration. GATK’s default downsampling option was suspended by setting “--downsampling_type NONE.” Variants were called with FreeBayes [21] (v1.1.0-46-g8d2b3a0) and VarScan2 [61] (v2.4.0) with their default settings.

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