Changes between Version 42 and Version 43 of ImputationPipeline

Timestamp:

Dec 6, 2011 1:11:58 PM (12 years ago)

Author:

a.kanterakis

Comment:

--

ImputationPipeline

@@ -70 +70 @@
 == References ==
  * Brian L. Browning, Sharon R. Browning. A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals. AJHG, Volume 84, Issue 2, 13 February 2009, Pages 210-223. doi:10.1016/j.ajhg.2009.01.005
+ * http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000529 Impute2
+ * http://www.biomedcentral.com/1471-2156/10/27 Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies
+ * The effect of genome-wide association scan quality control on imputation outcome for common variants. QC on scan quality has MINIMUM effect on imputation quality http://www.nature.com/ejhg/journal/v19/n5/full/ejhg2010242a.html , http://www.nature.com/ng/journal/v39/n7/full/ng2088.html Marchini , http://www.nature.com/nrg/journal/v11/n7/full/nrg2796.html
+ * Hickey JM, Kinghorn BP, Tier B, Wilson JF, Dunstan N, van der Werf JH. A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes. Genet Sel Evol. 2011 Mar 10;43:12. http://www.ncbi.nlm.nih.gov/pubmed/21388557
+ * The International HapMap Consortium. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52-58. 2010. The HapMap Project
+ * The use of imputation in GWAS studies: http://www.nature.com/ejhg/journal/v19/n2/full/ejhg2010157a.html?WT.i_dcsvid=%25%25LIST_ID%25%25-%25%25RECIPIENT_ID%25%25&WT.ec_id=MARKETING&WT.mc_id=EG1107CV030 Politopoulos I. et. al Genome-wide association of breast cancer: composite likelihood with imputed genotypes. European Journal of Human Genetics (2011) 19, 194–199.
+ * Introduction of imputation? http://www.ncbi.nlm.nih.gov/pubmed/19165921 Detection of sharing by descent, long-range phasing and haplotype imputation.
+ * We found that the difference between the unQCed data and the fully QCed data on imputation outcome was minimal. Our study shows that imputation of common variants is generally very accurate and robust to GWAS QC, which is not a major factor affecting imputation outcome. A minority of common-frequency SNPs with particular properties cannot be accurately imputed regardless of QC stringency. These findings may not generalise to the imputation of low frequency and rare variants. http://www.nature.com/ejhg/journal/v19/n5/full/ejhg2010242a.html . The effect of genome-wide association scan quality control on imputation outcome for common variants. European Journal of Human Genetics (2011) 19, 610–614.
 == See also ==
 * An older version of the imputation pipeline developed mainly by Harm-Jan and Lude Franke: [[ImputationPipeline_old]] it uses the [[ImputationTool]] for study / reference normalization.