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Revision as of 10:31, 4 September 2013
, 10:31, 4 September 2013→Required Reading
== Required Reading ==
== Required Reading ==
Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and
* Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and
missing-data inference for whole-genome association studies by use of localized
missing-data inference for whole-genome association studies by use of localized
haplotype clustering. ''Am J Hum Genet.'' '''81''':1084-97. PMID: 17924348
haplotype clustering. ''Am J Hum Genet.'' '''81''':1084-97. PMID: 17924348
Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson
* 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,
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,
Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V,
explosive population growth. ''Nat Commun.'' '''1''':131. PMID: 21119644
explosive population growth. ''Nat Commun.'' '''1''':131. PMID: 21119644
Delaneau O, Zagury JF, Marchini J (2013) Improved whole-chromosome phasing for
* Delaneau O, Zagury JF, Marchini J (2013) Improved whole-chromosome phasing for
disease and population genetic studies. ''Nat Methods.'' '''10''':5-6. PMID: 23269371
disease and population genetic studies. ''Nat Methods.'' '''10''':5-6. PMID: 23269371
Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate
* 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
genotype imputation in genome-wide association studies through pre-phasing. ''Nat
Genet.'' '''44''':955-9. PMID: 22820512
Genet.'' '''44''':955-9. PMID: 22820512
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G (2012) De novo assembly and
* 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.
genotyping of variants using colored de Bruijn graphs. ''Nat Genet.'' '''44''':226-32.
PMID: 22231483
PMID: 22231483
Jun G, Flickinger M, Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M,
* 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
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:
sequencing and array-based genotype data. ''Am J Hum Genet.'' '''91''':839-48. PMID:
23103226
23103226
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling
* 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
variants using mapping quality scores. ''Genome Res.'' '''18''':1851-8. PMID: 18714091
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler
* Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler
transform. ''Bioinformatics.'' '''25''':1754-60. PMID: 19451168
transform. ''Bioinformatics.'' '''25''':1754-60. PMID: 19451168
Li H, Durbin R (2011) Inference of human population history from individual
* Li H, Durbin R (2011) Inference of human population history from individual
whole-genome sequences. ''Nature.'' '''475''':493-6. PMID: 21753753
whole-genome sequences. ''Nature.'' '''475''':493-6. PMID: 21753753
Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and
* 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.''
genotype data to estimate haplotypes and unobserved genotypes. ''Genet Epidemiol.''
'''34''':816-34. PMID: 21058334
'''34''':816-34. PMID: 21058334
Lin DY, Zeng D (2010) Meta-analysis of genome-wide association studies: no
* 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.
efficiency gain in using individual participant data. ''Genet Epidemiol.'' '''34''':60-6.
PMID: 19847795
PMID: 19847795
Wen X, Stephens M (2010) Using linear predictors to impute allele frequencies from
* 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
summary or pooled genotype data. ''Ann Appl Stat.'' '''4''':1158-1182. PMID: 21479081
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly
* Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly
using de Bruijn graphs. ''Genome Res.'' '''18''':821-9. PMID: 18349386
using de Bruijn graphs. ''Genome Res.'' '''18''':821-9. PMID: 18349386
