PMID- 21903627
OWN - NLM
STAT- MEDLINE
DCOM- 20120313
LR  - 20240104
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 27
IP  - 21
DP  - 2011 Nov 1
TI  - A statistical framework for SNP calling, mutation discovery, association mapping 
      and population genetical parameter estimation from sequencing data.
PG  - 2987-93
LID - 10.1093/bioinformatics/btr509 [doi]
AB  - MOTIVATION: Most existing methods for DNA sequence analysis rely on accurate 
      sequences or genotypes. However, in applications of the next-generation 
      sequencing (NGS), accurate genotypes may not be easily obtained (e.g. 
      multi-sample low-coverage sequencing or somatic mutation discovery). These 
      applications press for the development of new methods for analyzing sequence data 
      with uncertainty. RESULTS: We present a statistical framework for calling SNPs, 
      discovering somatic mutations, inferring population genetical parameters and 
      performing association tests directly based on sequencing data without explicit 
      genotyping or linkage-based imputation. On real data, we demonstrate that our 
      method achieves comparable accuracy to alternative methods for estimating site 
      allele count, for inferring allele frequency spectrum and for association 
      mapping. We also highlight the necessity of using symmetric datasets for finding 
      somatic mutations and confirm that for discovering rare events, mismapping is 
      frequently the leading source of errors. AVAILABILITY: 
      http://samtools.sourceforge.net. CONTACT: hengli@broadinstitute.org.
FAU - Li, Heng
AU  - Li H
AD  - Medical Population Genetics Program, Broad Institute, 7 Cambridge Center, 
      Cambridge, MA 02142, USA. hengli@broadinstitute.org
LA  - eng
GR  - U01 HG005208/HG/NHGRI NIH HHS/United States
GR  - 1U01HG005208-01/HG/NHGRI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20110908
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - Alleles
MH  - Data Interpretation, Statistical
MH  - Gene Frequency
MH  - Genetic Association Studies
MH  - Genetics, Population/methods
MH  - Genotype
MH  - Humans
MH  - *Mutation
MH  - *Polymorphism, Single Nucleotide
MH  - *Sequence Analysis, DNA
PMC - PMC3198575
EDAT- 2011/09/10 06:00
MHDA- 2012/03/14 06:00
PMCR- 2012/11/01
CRDT- 2011/09/10 06:00
PHST- 2011/09/10 06:00 [entrez]
PHST- 2011/09/10 06:00 [pubmed]
PHST- 2012/03/14 06:00 [medline]
PHST- 2012/11/01 00:00 [pmc-release]
AID - btr509 [pii]
AID - 10.1093/bioinformatics/btr509 [doi]
PST - ppublish
SO  - Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. 
      Epub 2011 Sep 8.