DOI: 10.18129/B9.bioc.SICtools    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SICtools.

Find SNV/Indel differences between two bam files with near relationship

Bioconductor version: 3.9

This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

Author: Xiaobin Xing, Wu Wei

Maintainer: Xiaobin Xing <xiaobinxing0316 at>

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biocViews Alignment, Coverage, DataImport, QualityControl, SNP, SequenceMatching, Sequencing, Software, VariantDetection
Version 1.14.0
In Bioconductor since BioC 3.2 (R-3.2) (4 years)
License GPL (>=2)
Depends R (>= 3.0.0), methods, Rsamtools(>= 1.18.1), doParallel (>= 1.0.8), Biostrings(>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges(>= 1.22.4), IRanges(>= 2.4.8)
Suggests knitr, RUnit, BiocGenerics
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