ArticlePloS one2014
OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 30 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Placental-Cadherin, a biomarker for local immune status and poor prognosis among patients with tongue squamous cell carcinoma.European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery · 2022Pooled it
- A key SNP in the flavonoid biosynthesis pathway gene CsaV3_6G009030 is highly correlated with cucumber fruit bitterness.Food chemistry. Molecular sciences · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- The Genetic Loci Associated with Fiber Development in Upland Cotton (Plants (Basel, Switzerland) · 2025Article
- Identification of Growth-Related SNPs and Candidate Genes in the Genome of Zig-Zag Eel (Mastacembelus armatus) by GWAS.Marine biotechnology (New York, N.Y.) · 2025Article
- Genetic diversity analysis and core germplasm construction of tea plants in Lu'an.BMC plant biology · 2025Article
- Genome-Wide Association Study Reveals Growth-Related SNPs and Candidate Genes in Largemouth Bass (International journal of molecular sciences · 2025Article
- Drivers of intraspecific genetic differentiation of a wheat's wild relativeFrontiers in plant science · 2025Article
- Population genetic diversity and environmental adaptation of Tamarix hispida in the Tarim Basin, arid Northwestern China.Heredity · 2024Article
- A novel SNP within the Rsa10025320 gene is highly associated with hollowness in red-skinned radish fleshy roots.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Integration of Whole-Genome Resequencing and Transcriptome Sequencing Reveals Candidate Genes in High Glossiness of Eggshell.Animals : an open access journal from MDPI · 2024Article
- Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness.The ISME journal · 2023Article
- Design combinations of evolved phage and antibiotic for antibacterial guided by analyzing the phage resistance of poorly antimicrobial phage.Microbiology spectrum · 2023Article
- Characterization of two O-methyltransferases involved in the biosynthesis of O-methylated catechins in tea plant.Nature communications · 2023Article
- Article
- Functional analysis of CqPORB in the regulation of chlorophyll biosynthesis inFrontiers in plant science · 2022Article
- OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow.BMC bioinformatics · 2021Article
- CsUFO is involved in the formation of flowers and tendrils in cucumber.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Review
- Transcriptome profiling of venom gland from wasp species: de novo assembly, functional annotation, and discovery of molecular markers.BMC genomics · 2020Article
- Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato.BMC plant biology · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.