Article
Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project.
Scientific reports - 25 Mar 2024
Gong Binsheng, Li Dan, Zhang Yifan, Kusko Rebecca, Lababidi Samir, Cao Zehui, Chen Mingyang, Chen Ning, Chen Qiaochu, Chen Qingwang, Dai Jiacheng, Gan Qiang, Gao Yuechen, Guo Mingkun, Hariani Gunjan, He Yujie, Hou Wanwan, Jiang He, Kushwaha Garima, Li Jian-Liang, Li Jianying, Li Yulan, Liu Liang-Chun, Liu Ruimei, Liu Shiming, Meriaux Edwin, Mo Mengqing, Moore Mathew, Moss Tyler J, Niu Quanne, Patel Ananddeep, Ren Luyao, Saremi Nedda F, Shang Erfei, Shang Jun, Song Ping, Sun Siqi, Urban Brent J, Wang Danke, Wang Shangzi, Wen Zhining, Xiong Xiangyi, Yang Jingcheng, Yin Lihui, Zhang Chao, Zhang Ruolan, Bhandari Ambica, Cai Wanshi, Eterovic Agda Karina, Megherbi Dalila B, Shi Tieliu, Suo Chen, Yu Ying, Zheng Yuanting, Novoradovskaya Natalia, Sears Renee L, Shi Leming, Jones Wendell, Tong Weida, Xu Joshua
Abstract excerpt
Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited. This project sought to...
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