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

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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
Date of publication
None
Maintainer
Xiaobin Xing <xiaobinxing0316@gmail.com>
License
GPL (>=2)
Version
1.4.0

View on Bioconductor

Man pages

indelDiff
main function to call indel difference between the bam files
SICtools-package
tools for SNV/Indel Comparison between two bam files with...
snpDiff
main function to test point differences between the two bam...

Files in this package

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