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The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. Li H, et al. Among authors: marth g. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. Bioinformatics. 2009. PMID: 19505943 Free PMC article.
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Danecek P, et al. Among authors: marth gt. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. Bioinformatics. 2011. PMID: 21653522 Free PMC article.
Sequence assembly with CAFTOOLS.
Dear S, Durbin R, Hillier L, Marth G, Thierry-Mieg J, Mott R. Dear S, et al. Among authors: marth g. Genome Res. 1998 Mar;8(3):260-7. doi: 10.1101/gr.8.3.260. Genome Res. 1998. PMID: 9521929 Free PMC article.
The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium. Clarke L, et al. Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974. Nat Methods. 2012. PMID: 22543379 Free PMC article.
A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium; Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. 1000 Genomes Project Consortium, et al. Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534. Nature. 2010. PMID: 20981092 Free PMC article.
Diversity of human copy number variation and multicopy genes.
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project; Eichler EE. Sudmant PH, et al. Science. 2010 Oct 29;330(6004):641-6. doi: 10.1126/science.1197005. Science. 2010. PMID: 21030649 Free PMC article.
Mapping copy number variation by population-scale genome sequencing.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project. Mills RE, et al. Among authors: marth gt. Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708. Nature. 2011. PMID: 21293372 Free PMC article.
Variation in genome-wide mutation rates within and between human families.
Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P; 1000 Genomes Project. Conrad DF, et al. Nat Genet. 2011 Jun 12;43(7):712-4. doi: 10.1038/ng.862. Nat Genet. 2011. PMID: 21666693 Free PMC article.
Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium; Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Khurana E, et al. Among authors: marth g. Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587. Science. 2013. PMID: 24092746 Free PMC article.
157 results