{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T10:23:30Z","timestamp":1783333410386,"version":"3.54.6"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"S5","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,3]]},"DOI":"10.1186\/s12859-017-1537-8","type":"journal-article","created":{"date-parts":[[2017,3,23]],"date-time":"2017-03-23T11:23:36Z","timestamp":1490268216000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":109,"title":["GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data"],"prefix":"10.1186","volume":"18","author":[{"given":"Simona","family":"De Summa","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni","family":"Malerba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosamaria","family":"Pinto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Mori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladan","family":"Mijatovic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefania","family":"Tommasi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,3,23]]},"reference":[{"key":"1537_CR1","first-page":"602","volume":"14","author":"M Chan","year":"2012","unstructured":"Chan M, Ji SM, Yeo ZX, Gan L, Yap E, Yap YS, Ng R, Tan PH, Ho GH, Ang P, Lee ASG. Development of a next-generation sequencing method for BRCA mutation screening: a comparison between a high-throughput and a benchtop platform. J MolDiagn. 2012;14:602\u201312.","journal-title":"J MolDiagn"},{"key":"1537_CR2","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1002\/humu.22272","volume":"34","author":"JL Costa","year":"2013","unstructured":"Costa JL, Sousa S, Justino A, Kay T, Fernandes S, Cirnes L, Schmitt F, Machado JC. Nonoptical massive parallel DNA sequencing of BRCA1 and BRCA2 genes in a diagnostic setting. Hum Mutat. 2013;34:629\u201335.","journal-title":"Hum Mutat"},{"key":"1537_CR3","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1038\/nature10242","volume":"475","author":"JM Rothberg","year":"2011","unstructured":"Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475:348\u201352.","journal-title":"Nature"},{"key":"1537_CR4","first-page":"234","volume":"15","author":"AG Hadd","year":"2013","unstructured":"Hadd AG, Houghton J, Choudhary A, Sah S, Chen L, Marko AC, Sanford T, Buddavarapu K, Krosting J, Garmire L, Wylie D, Shinde R, Beaudenon S, Alexander EK, Mambo E, Adai AT, Latham GJ. Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens. J MolDiagn. 2013;15:234\u201347.","journal-title":"J MolDiagn"},{"key":"1537_CR5","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1378\/chest.12-1917","volume":"143","author":"SA Yousem","year":"2013","unstructured":"Yousem SA, Dacic S, Nikiforov YE, Nikiforova M. Pulmonary Langerhans cell histiocytosis: profiling of multifocal tumors using next-generation sequencing identifies concordant occurrence of BRAF V600E mutations. Chest. 2013;143:1679\u201384.","journal-title":"Chest"},{"key":"1537_CR6","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/nbt.2522","volume":"31","author":"S J\u00fcnemann","year":"2013","unstructured":"J\u00fcnemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D. Updating benchtop sequencing performance comparison. Nat Biotechnol. 2013;31:294\u20136.","journal-title":"Nat Biotechnol"},{"key":"1537_CR7","volume":"7","author":"ZX Yeo","year":"2012","unstructured":"Yeo ZX, Chan M, Yap YS, Ang P, Rozen S, Lee ASG. Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer. PLoS One. 2012;7, e45798.","journal-title":"PLoS One"},{"key":"1537_CR8","doi-asserted-by":"crossref","first-page":"24","DOI":"10.7171\/jbt.12-2301-003","volume":"23","author":"AM Elliott","year":"2012","unstructured":"Elliott AM, Radecki J, Moghis B, Li X, Kammesheidt A. Rapid detection of the ACMG\/ACOG-recommended 23 CFTR disease-causing mutations using ion torrent semiconductor sequencing. JBiomol Tech. 2012;23:24\u201330.","journal-title":"JBiomol Tech"},{"key":"1537_CR9","first-page":"e1003031","volume":"9","author":"LM Bragg","year":"2013","unstructured":"Bragg LM, Stone G, Butler MK, Hugenholtz P, Tyson GW. Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. PLoSComputBiol. 2013;9:e1003031.","journal-title":"PLoSComputBiol"},{"key":"1537_CR10","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/nrg2986","volume":"12","author":"R Nielsen","year":"2011","unstructured":"Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet. 2011;12:443\u201351.","journal-title":"Nat Rev Genet"},{"key":"1537_CR11","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.1093\/bioinformatics\/btr477","volume":"27","author":"M Ruffalo","year":"2011","unstructured":"Ruffalo M, LaFramboise T, Koyut\u00fcrk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics. 2011;27:2790\u20136.","journal-title":"Bioinformatics"},{"key":"1537_CR12","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0030080","volume":"7","author":"S Pattnaik","year":"2012","unstructured":"Pattnaik S, Vaidyanathan S, Pooja DG, Deepak S, Panda B. Customisation of the exome data analysis pipeline using a combinatorial approach. PLoS One. 2012;7, e30080.","journal-title":"PLoS One"},{"key":"1537_CR13","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1186\/1471-2164-15-264","volume":"15","author":"S Caboche","year":"2014","unstructured":"Caboche S, Audebert C, Lemoine Y, Hot D. Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data. BMC Genomics. 2014;15:264.","journal-title":"BMC Genomics"},{"key":"1537_CR14","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1186\/1471-2164-15-516","volume":"15","author":"ZX Yeo","year":"2014","unstructured":"Yeo ZX, Wong JCL, Rozen SG, Lee ASG. Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes. BMC Genomics. 2014;15:516.","journal-title":"BMC Genomics"},{"issue":"4","key":"1537_CR15","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","volume":"28","author":"W Huang","year":"2012","unstructured":"Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012;28(4):593\u20134.","journal-title":"Bioinformatics"},{"issue":"9","key":"1537_CR16","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genomeresearch. 2010;20(9):1297\u2013303. doi: 10.1101\/gr.107524.110 .","journal-title":"Genomeresearch"},{"issue":"14","key":"1537_CR17","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754\u201360. doi: 10.1093\/bioinformatics\/btp324 .","journal-title":"Bioinformatics"},{"key":"1537_CR18","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/nbt.2835","volume":"32","author":"JM Zook","year":"2014","unstructured":"Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, Salit M. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014;32:246\u201351.","journal-title":"Nat Biotechnol"},{"key":"1537_CR19","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1186\/1471-2164-15-244","volume":"15","author":"H Xu","year":"2014","unstructured":"Xu H, DiCarlo J, Satya RV, Peng Q, Wang Y. Comparison of somatic mutation calling methods in amplicon and whole exome sequence data. BMC Genomics. 2014;15:244.","journal-title":"BMC Genomics"},{"key":"1537_CR20","doi-asserted-by":"crossref","first-page":"28765","DOI":"10.3390\/ijms161226129","volume":"16","author":"I Vanni","year":"2015","unstructured":"Vanni I, Coco S, Truini A, Rusmini M, Dal Bello MG, Alama A, Banelli B, Mora M, Rijavec E, Barletta G, Genova C, Biello F, Maggioni C, Grossi F. Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGMTM Platform. Int J MolSci. 2015;16:28765\u201382.","journal-title":"Int J MolSci"},{"key":"1537_CR21","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.112326.110","volume":"21","author":"CA Albers","year":"2011","unstructured":"Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R. Dindel: accurate indel calls from short-read data. Genome Res. 2011;21:961\u201373.","journal-title":"Genome Res"},{"key":"1537_CR22","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/1471-2105-15-125","volume":"15","author":"AR Carson","year":"2014","unstructured":"Carson AR, Smith EN, Matsui H, Br\u00e6kkan SK, Jepsen K, Hansen J-B, Frazer KA. Effective filtering strategies to improve data quality from population-based whole exome sequencing studies. BMC Bioinformatics. 2014;15:125.","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1537-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,25]],"date-time":"2017-06-25T13:17:27Z","timestamp":1498396647000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1537-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3]]},"references-count":22,"journal-issue":{"issue":"S5","published-print":{"date-parts":[[2017,3]]}},"alternative-id":["1537"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1537-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3]]},"article-number":"119"}}