ライフサイエンスコーパス: genotype calling

1 e-phasing WGS reference panels after initial genotype calling.

2 out association testing without intermediate genotype calling.

3 ments in read mapping, variant discovery and genotype calling.

4 supports development of improved methods for genotype calling.

5 containing subsets of the entire dataset for genotype calling.

6 ing population stratification, and improving genotype calling.

7 mulations, we show that trios provide higher genotype calling accuracy across the frequency spectrum,

8 multiple offspring can dramatically increase genotype calling accuracy and reduce phasing and Mendeli

9 igh Density (SNiPer-HD), for highly accurate genotype calling across hundreds of thousands of SNPs.

10 ize and batch composition for effects on the genotype calling algorithm BRLMM using raw data of 270 H

11 iva (domestic rice), we have developed a new genotype calling algorithm called 'ALCHEMY' based on sta

12 veloped an integrated multi-SNP, multi-array genotype calling algorithm for Affymetrix SNP arrays, MA

13 Here, we present a fast and accurate genotype calling algorithm for the Illumina BeadArray ge

14 We have introduced a model-based genotype calling algorithm which does not rely on having

15 We have developed a novel genotype-calling algorithm for the Illumina platform, op

16 Here, we propose a novel genotype-calling algorithm that, in contrast to the othe

17 Standard genotype calling algorithms are less likely to call rare

18 Most genotype calling algorithms currently used for GWAS are

19 Existing microarray genotype-calling algorithms adopt either SNP-by-SNP (SNP

20 ot rely on single-nucleotide polymorphism or genotype calling and are particularly suitable for low s

21 ads affect the downstream variant discovery, genotype calling and association analysis.

22 inD) study, we identify a source of error in genotype calling and demonstrate that a standard battery

23 the development of methods capable of joint genotype calling and haplotype assembly.

24 We anticipate our method will facilitate genotype calling and haplotype inference for many ongoin

25 We develop a new probabilistic model for genotype calling and haplotype phasing from NGS data tha

26 Bayesian Markov model (DBM) for simultaneous genotype calling and haplotype phasing in low-coverage N

27 Although our model improves the accuracy of genotype calling and haplotype phasing, haplotype inform

28 eta-analysis of European ancestry by refined genotype calling and imputation and by the addition of 5

29 Accuracy of genotype calling and imputation were high with both simu

30 g data, read mapping, inference of RAD loci, genotype calling, and filtering of the output data, as w

31 Some simple approaches for genotype calling apply fixed filters, such as calling a

32 eqEM offers an improved, robust and flexible genotype-calling approach that can be widely applied in

33 Highly accurate and reproducible genotype calling are paramount since errors introduced b

34 ropose methods to model contamination during genotype calling as an alternative to removal of contami

35 ods, that can account for the uncertainty in genotype-calling associated with Next Generation Sequenc

36 When sequencing a set of individuals, genotype calling can be challenging due to low sequencin

37 oaches, RefEditor can significantly increase genotype calling consistency (from 43% to 61% at 4X cove

38 formed a comprehensive analysis to study how genotype calling errors affect type I error and statisti

39 We concluded that non-symmetric genotype calling errors need careful consideration in th

40 In simulation studies, we found that biased genotype calling errors yielded not only an inflation of

41 haplotype construction and imputation-based genotype calling, even without the availability of large

42 We used these data to establish genotype-calling filters that dramatically increase accu

43 netic studies, researchers typically perform genotype calling first and then apply standard genotype-

44 Accurate genotype calling for high throughput Illumina data is an

45 perior performance for haplotype phasing and genotype calling for population NGS data over existing m

46 Genotype calling from high-throughput platforms such as

47 Simultaneous genotype calling from low-coverage sequence data and imp

48 xisting approaches for haplotype phasing and genotype-calling from short read data.

49 everal tools have been developed for SNP and genotype calling in NGS data, haplotype phasing is often

50 ng genotype cluster plots to verify sensible genotype calling in putatively associated single nucleot

51 Here, we describe a method for genotype calling in settings where sequence data are ava

52 Accurate genotype calling is a pre-requisite of a successful Geno

53 kage disequilibrium (LD) based refinement of genotyping calling is essential to improve the accuracy.

54 The R code for the family-based genotype calling methods (SNPCaller) is available to be

55 However, genotype-calling methods for family-based sequence data,

56 Other genotype-calling methods, such as MAQ and SOAPsnp, are i

57 using external panels can greatly facilitate genotype calling of sequencing data with a small number

58 oach is demonstrated through applications to genotype calling on a set of HapMap samples used for qua

59 t take advantage of specific features of the genotype calling problem.

60 us, which induces uncertainty in the SNP and genotype calling procedures and, ultimately, adversely a

61 We have developed a novel SNP genotype calling program, SNiPer-High Density (SNiPer-HD

62 In order to improve variant detection and genotype calling, raw sequence data are typically examin

63 hat both batch size and composition affected genotype calling results and significantly associated SN

64 Batch size and composition affect the genotype calling results in GWAS using BRLMM.

65 Microarrays are the genotype calling technology of choice in GWAS as they pe

66 However, such a two-step approach ignores genotype calling uncertainty in the association testing

67 These methods take genotype calling uncertainty into account by directly in