Subclonal variant calling with multiple samples and prior knowledge
نویسندگان
چکیده
منابع مشابه
Subclonal variant calling with multiple samples and prior knowledge
MOTIVATION Targeted resequencing of cancer genes in large cohorts of patients is important to understand the biological and clinical consequences of mutations. Cancers are often clonally heterogeneous, and the detection of subclonal mutations is important from a diagnostic point of view, but presents strong statistical challenges. RESULTS Here we present a novel statistical approach for calli...
متن کاملSubclonal variant calling with multiple samples and prior knowledge using shearwater
2 The statistical model 1 2.1 Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2.2 Testing for variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2.2.1 The OR model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2.2.2 The AND model . . . . . . . . . . . . . . . . . . . . ...
متن کاملCalling subclonal mutations with deepSNV
This package provides algorithms for calling single nucleotide variants in deep sequencing experiments of polyclonal samples. The package uses a clonal control experiment for estimating the local error rate and tests whether the observed nucleotide frequencies differ between test and control. The basic model is a binomial model for the counts Xi,j and Yi,j of nucleotide j at position i, in the ...
متن کاملRare variant discovery and calling by sequencing pooled samples with overlaps
MOTIVATION For many complex traits/diseases, it is believed that rare variants account for some of the missing heritability that cannot be explained by common variants. Sequencing a large number of samples through DNA pooling is a cost-effective strategy to discover rare variants and to investigate their associations with phenotypes. Overlapping pool designs provide further benefit because such...
متن کاملS 6 Structural Variant Calling
S6.1 Genome-wide Structural Variant Detection We used whole-genome shotgun paired-end sequence data generated with both Illumina and Applied Biosystems SOLiD platforms from the genomes of six canid samples (including a additional Basenji only sequenced to low coverage on the Illumina platform, but excluding the Chinese wolf), to estimate the fraction of the genome with segmental duplications. O...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2014
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btt750