TY - JOUR AU - Doig, K. AU - Papenfuss, A. T. AU - Fox, S. PY - 2015 DA - 2015// TI - Clinical cancer genomic analysis: data engineering required JO - The Lancet Oncology VL - 16 UR - https://doi.org/10.1016/S1470-2045(15)00195-3 DO - 10.1016/S1470-2045(15)00195-3 ID - Doig2015 ER - TY - STD TI - Docker. Docker containerisation site, http:/http://www.docker.com. Accessed 29 Nov 2017. UR - http://www.docker.com ID - ref2 ER - TY - STD TI - Park DJ, et al. UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing. BMC bioinformatics. 2016;17:165. doi:10.1186/s12859-016-1014-9. Accessed 29 Nov 2017. ID - ref3 ER - TY - JOUR AU - Yost, S. E. PY - 2013 DA - 2013// TI - Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt305 DO - 10.1093/bioinformatics/btt305 ID - Yost2013 ER - TY - STD TI - Illumina. https://basespace.illumina.com. UR - https://basespace.illumina.com ID - ref5 ER - TY - JOUR AU - Hsu, A. L. PY - 2015 DA - 2015// TI - AmpliVar: mutation detection in high-throughput sequence from amplicon-based libraries JO - Hum Mutat VL - 36 UR - https://doi.org/10.1002/humu.22763 DO - 10.1002/humu.22763 ID - Hsu2015 ER - TY - STD TI - FASTQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. UR - http://www.bioinformatics.babraham.ac.uk/projects/fastqc ID - ref7 ER - TY - JOUR AU - Wong, S. Q. PY - 2015 DA - 2015// TI - Assessing the clinical value of targeted massively parallel sequencing in a longitudinal, prospective population-based study of cancer patients JO - Br J Cancer VL - 112 UR - https://doi.org/10.1038/bjc.2015.80 DO - 10.1038/bjc.2015.80 ID - Wong2015 ER - TY - JOUR AU - Zhao, M. AU - Lee, W. P. AU - Garrison, E. P. AU - Marth, G. T. PY - 2013 DA - 2013// TI - SSW library: an SIMD smith-waterman C/C++ library for use in genomic applications JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0082138 DO - 10.1371/journal.pone.0082138 ID - Zhao2013 ER - TY - STD TI - HGVS. HGVS Nomenclature, http://varnomen.hgvs.org. Accessed 29 Nov 2017. UR - http://varnomen.hgvs.org ID - ref10 ER - TY - JOUR AU - Rehm, H. L. PY - 2013 DA - 2013// TI - ACMG clinical laboratory standards for next-generation sequencing JO - Genetics in medicine : official journal of the American College of Medical Genetics VL - 15 UR - https://doi.org/10.1038/gim.2013.92 DO - 10.1038/gim.2013.92 ID - Rehm2013 ER - TY - JOUR AU - Tan, A. AU - Abecasis, G. R. AU - Kang, H. M. PY - 2015 DA - 2015// TI - Unified representation of genetic variants JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv112 DO - 10.1093/bioinformatics/btv112 ID - Tan2015 ER - TY - STD TI - Mutalyzer. https://mutalyzer.nl. UR - https://mutalyzer.nl ID - ref13 ER - TY - JOUR AU - McCarthy, D. J. PY - 2014 DA - 2014// TI - Choice of transcripts and software has a large effect on variant annotation JO - Genome medicine VL - 6 UR - https://doi.org/10.1186/gm543 DO - 10.1186/gm543 ID - McCarthy2014 ER - TY - JOUR AU - Wang, K. AU - Li, M. AU - Hakonarson, H. PY - 2010 DA - 2010// TI - ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq603 DO - 10.1093/nar/gkq603 ID - Wang2010 ER - TY - JOUR AU - Yang, H. AU - Wang, K. PY - 2015 DA - 2015// TI - Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR JO - Nat Protoc VL - 10 UR - https://doi.org/10.1038/nprot.2015.105 DO - 10.1038/nprot.2015.105 ID - Yang2015 ER - TY - JOUR AU - Cingolani, P. PY - 2012 DA - 2012// TI - A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff JO - Fly VL - 6 UR - https://doi.org/10.4161/fly.19695 DO - 10.4161/fly.19695 ID - Cingolani2012 ER - TY - JOUR AU - McLaren, W. PY - 2010 DA - 2010// TI - Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq330 DO - 10.1093/bioinformatics/btq330 ID - McLaren2010 ER - TY - STD TI - MyVariant. http://myvariant.info. Accessed 29 Nov 2017. UR - http://myvariant.info ID - ref19 ER - TY - JOUR AU - Xin, J. PY - 2016 DA - 2016// TI - High-performance web services for querying gene and variant annotation JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-0953-9 DO - 10.1186/s13059-016-0953-9 ID - Xin2016 ER - TY - JOUR AU - Kircher, M. PY - 2014 DA - 2014// TI - A general framework for estimating the relative pathogenicity of human genetic variants JO - Nat Genet VL - 46 UR - https://doi.org/10.1038/ng.2892 DO - 10.1038/ng.2892 ID - Kircher2014 ER - TY - JOUR AU - Quinlan, A. R. AU - Hall, I. M. PY - 2010 DA - 2010// TI - BEDTools: a flexible suite of utilities for comparing genomic features JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq033 DO - 10.1093/bioinformatics/btq033 ID - Quinlan2010 ER - TY - STD TI - NA12878. Genome in a bottle consortium, http://www.genomeinabottle.org. Accessed 29 Nov 2017. UR - http://www.genomeinabottle.org ID - ref23 ER - TY - STD TI - Acrometrix, Thermofisher, https://www.thermofisher.com/au/en/home/brands/product-brand/acrometrix.html. Accessed 29 Nov 2017 UR - https://www.thermofisher.com/au/en/home/brands/product-brand/acrometrix.html ID - ref24 ER - TY - STD TI - Coriell Institute, GM24385, https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM24385&Product=CC. Accessed 29 Nov 2017. UR - https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM24385&Product=CC ID - ref25 ER - TY - JOUR AU - Doig, K. D. PY - 2017 DA - 2017// TI - PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories JO - Genome medicine VL - 9 UR - https://doi.org/10.1186/s13073-017-0427-z DO - 10.1186/s13073-017-0427-z ID - Doig2017 ER - TY - STD TI - Groovy. The Groovy Language, http://www.groovy-lang.org. Accessed 29 Nov 2017. UR - http://www.groovy-lang.org ID - ref27 ER - TY - STD TI - GNU General Public License https://www.gnu.org/licenses/ - GPL. Accessed 29 Nov 2017. UR - https://www.gnu.org/licenses ID - ref28 ER -