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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SICtools")
AuthorXiaobin Xing, Wu Wei
Bioconductor views Alignment Coverage DataImport QualityControl SNP SequenceMatching Sequencing Software VariantDetection
Date of publicationNone
MaintainerXiaobin Xing <xiaobinxing0316@gmail.com>
LicenseGPL (>=2)
Version1.4.0

View on Bioconductor

Files

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/SICtools-internal.R R/indelDiff.R R/snpDiff.R
build
build/vignette.rds
inst
inst/doc
inst/doc/SICtools.R
inst/doc/SICtools.Rmd
inst/doc/SICtools.pdf
inst/extdata
inst/extdata/example.ref.fasta
inst/extdata/example.ref.fasta.fai
inst/extdata/example1.bam
inst/extdata/example1.bam.bai
inst/extdata/example2.bam
inst/extdata/example2.bam.bai
inst/unitTests
inst/unitTests/runTests.R inst/unitTests/test_indelDiff.R inst/unitTests/test_snpDiff.R
man
man/SICtools-package.Rd man/indelDiff.Rd man/snpDiff.Rd
src
src/AUTHORS
src/COPYING
src/ChangeLog.old
src/INSTALL
src/Makefile
src/Makefile.mingw
src/NEWS
src/bam.c
src/bam.h
src/bam2bcf.c
src/bam2bcf.h
src/bam2bcf_indel.c
src/bam2depth.c
src/bam_aux.c
src/bam_cat.c
src/bam_color.c
src/bam_endian.h
src/bam_import.c
src/bam_index.c
src/bam_lpileup.c
src/bam_mate.c
src/bam_md.c
src/bam_pileup.c
src/bam_plcmd.c
src/bam_reheader.c
src/bam_rmdup.c
src/bam_rmdupse.c
src/bam_sort.c
src/bam_stat.c
src/bam_tview.c
src/bam_tview.h
src/bam_tview_curses.c
src/bam_tview_html.c
src/bamshuf.c
src/bamtk.c
src/bcftools
src/bcftools/Makefile
src/bcftools/README
src/bcftools/bcf.c
src/bcftools/bcf.h
src/bcftools/bcf.tex
src/bcftools/bcf2qcall.c
src/bcftools/bcfutils.c
src/bcftools/call1.c
src/bcftools/em.c
src/bcftools/fet.c
src/bcftools/index.c
src/bcftools/kfunc.c
src/bcftools/kmin.c
src/bcftools/kmin.h
src/bcftools/main.c
src/bcftools/mut.c
src/bcftools/prob1.c
src/bcftools/prob1.h
src/bcftools/vcf.c
src/bcftools/vcfutils.pl
src/bedcov.c
src/bedidx.c
src/bgzf.c
src/bgzf.h
src/bgzip.c
src/chk_indel.c
src/cut_target.c
src/errmod.c
src/errmod.h
src/examples
src/examples/00README.txt
src/examples/Makefile
src/examples/bam2bed.c
src/examples/calDepth.c
src/examples/chk_indel.c
src/examples/ex1.fa
src/examples/ex1.sam.gz
src/examples/toy.fa
src/examples/toy.sam
src/faidx.c
src/faidx.h
src/install.libs.R
src/kaln.c
src/kaln.h
src/khash.h
src/klist.h
src/knetfile.c
src/knetfile.h
src/kprobaln.c
src/kprobaln.h
src/kseq.h
src/ksort.h
src/kstring.c
src/kstring.h
src/misc
src/misc/HmmGlocal.java
src/misc/Makefile
src/misc/ace2sam.c
src/misc/bamcheck.c
src/misc/blast2sam.pl
src/misc/bowtie2sam.pl
src/misc/export2sam.pl
src/misc/interpolate_sam.pl
src/misc/maq2sam.c
src/misc/md5.c
src/misc/md5.h
src/misc/md5fa.c
src/misc/novo2sam.pl
src/misc/plot-bamcheck
src/misc/psl2sam.pl
src/misc/r2plot.lua
src/misc/sam2vcf.pl
src/misc/samtools.pl
src/misc/soap2sam.pl
src/misc/varfilter.py
src/misc/vcfutils.lua
src/misc/wgsim.c
src/misc/wgsim_eval.pl
src/misc/zoom2sam.pl
src/padding.c
src/phase.c
src/razf.c
src/razf.h
src/razip.c
src/sam.c
src/sam.h
src/sam_header.c
src/sam_header.h
src/sam_view.c
src/sample.c
src/sample.h
src/samtools.1
src/win32
src/win32/xcurses.h
src/win32/zconf.h
src/win32/zlib.h
tests
tests/runTests.R
vignettes
vignettes/SICtools.Rmd

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