OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data

Pengyuan Zhu; Lingyu He; Yaqiao Li; Wenpan Huang; Feng Xi; Lin Lin; Qihuan Zhi; Wenwei Zhang; Y Tom Tang; Chunyu Geng; Zhiyuan Lu; Xun Xu

doi:10.1371/journal.pone.0097507

OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data

PLoS One. 2014 May 13;9(5):e97507. doi: 10.1371/journal.pone.0097507. eCollection 2014.

Authors

Pengyuan Zhu¹, Lingyu He¹, Yaqiao Li¹, Wenpan Huang¹, Feng Xi¹, Lin Lin¹, Qihuan Zhi¹, Wenwei Zhang¹, Y Tom Tang², Chunyu Geng¹, Zhiyuan Lu¹, Xun Xu¹

Affiliations

¹ BGI-Shenzhen, Shenzhen, China.
² Complete Genomics, Inc., Mountain View, California, United States of America.

Abstract

Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly. We developed an optimized SNP calling method using TMAP and GATK (OTG-snpcaller). This method combined our own optimized processes, Remove Duplicates According to AS Tag (RDAST) and Alignment Optimize Structure (AOS), together with TMAP and GATK, to call SNPs from Proton data. We sequenced four sets of exomes captured by Agilent SureSelect and NimbleGen SeqCap EZ Kit, using Life Technology's Ion Proton sequencer. Then we applied OTG-snpcaller and compared our results with the results from Torrent Variants Caller. The results indicated that OTG-snpcaller can reduce both false positive and false negative rates. Moreover, we compared our results with Illumina results generated by GATK best practices, and we found that the results of these two platforms were comparable. The good performance in variant calling using GATK best practices can be primarily attributed to the high quality of the Illumina sequences.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Exome / genetics
Genome, Human / genetics*
High-Throughput Nucleotide Sequencing / methods*
Humans
Molecular Sequence Data
Polymorphism, Single Nucleotide / genetics*
Sequence Alignment / methods
Sequence Analysis, DNA / instrumentation*
Sequence Analysis, DNA / methods*
Software*

Grants and funding

This project was supported by The National High Technology Research and Development Program of China - 863 Program (NO.2012AA02A201); Shenzhen Key Laboratory of Transomics Biotechnologies (NO.CXB201108250096A). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.