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Revision as of 10:25, 4 September 2013
, 10:25, 4 September 2013→Required Reading
== Required Reading ==
== Required Reading ==
Delaneau O, Zagury JF, Marchini J (2013) Improved whole-chromosome phasing for
disease and population genetic studies. Nat Methods. 10:5-6. PMID: 23269371
Jun G, Flickinger M, Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M,
Kang HM (2012) Detecting and estimating contamination of human DNA samples in
sequencing and array-based genotype data. Am J Hum Genet. 91:839-48. PMID:
23103226
Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate
genotype imputation in genome-wide association studies through pre-phasing. Nat
Genet. 44:955-9. PMID: 22820512
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G (2012) De novo assembly and
genotyping of variants using colored de Bruijn graphs. Nat Genet. 44:226-32.
PMID: 22231483
Li H, Durbin R (2011) Inference of human population history from individual
whole-genome sequences. Nature. 475:493-6. PMID: 21753753
Wen X, Stephens M (2010) Using linear predictors to impute allele frequencies from
summary or pooled genotype data. Ann Appl Stat. 4:1158-1182. PMID: 21479081
Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson
JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H,
Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V,
Santibanez J, Morgan M, Chang K, Iv WH, Templeton AR, Boerwinkle E, Gibbs R, Sing
CF (2010) Deep resequencing reveals excess rare recent variants consistent with
explosive population growth. Nat Commun. 1:131. PMID: 21119644
Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and
genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol.
34:816-34. PMID: 21058334
Lin DY, Zeng D (2010) Meta-analysis of genome-wide association studies: no
efficiency gain in using individual participant data. Genet Epidemiol. 34:60-6.
PMID: 19847795
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler
transform. Bioinformatics. 25:1754-60. PMID: 19451168
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling
variants using mapping quality scores. Genome Res. 18:1851-8. PMID: 18714091
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly
using de Bruijn graphs. Genome Res. 18:821-9. PMID: 18349386
Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and
missing-data inference for whole-genome association studies by use of localized
haplotype clustering. Am J Hum Genet. 81:1084-97. PMID: 17924348
== Course History ==
== Course History ==
This course is an ad-hoc course, first taught by Goncalo Abecasis in the Fall of 2013.
This course is an ad-hoc course, first taught by Goncalo Abecasis in the Fall of 2013.
