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Tools (written in C using htslib) for manipulating next-generation sequencing data

samtools.sourceforge.net/

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.travis
.travis
 
 
examples
examples
 
 
misc
misc
 
 
test
test
 
 
win32
win32
 
 
.gitattributes
.gitattributes
 
 
.gitignore
.gitignore
 
 
.travis.yml
.travis.yml
 
 
AUTHORS
AUTHORS
 
 
ChangeLog.old
ChangeLog.old
 
 
INSTALL
INSTALL
 
 
LICENSE
LICENSE
 
 
Makefile
Makefile
 
 
Makefile.mingw
Makefile.mingw
 
 
NEWS
NEWS
 
 
README
README
 
 
README.md
README.md
 
 
bam.c
bam.c
 
 
bam.h
bam.h
 
 
bam2bcf.c
bam2bcf.c
 
 
bam2bcf.h
bam2bcf.h
 
 
bam2bcf_indel.c
bam2bcf_indel.c
 
 
bam2depth.c
bam2depth.c
 
 
bam_addrprg.c
bam_addrprg.c
 
 
bam_aux.c
bam_aux.c
 
 
bam_cat.c
bam_cat.c
 
 
bam_color.c
bam_color.c
 
 
bam_endian.h
bam_endian.h
 
 
bam_flags.c
bam_flags.c
 
 
bam_import.c
bam_import.c
 
 
bam_index.c
bam_index.c
 
 
bam_lpileup.c
bam_lpileup.c
 
 
bam_lpileup.h
bam_lpileup.h
 
 
bam_mate.c
bam_mate.c
 
 
bam_md.c
bam_md.c
 
 
bam_plbuf.c
bam_plbuf.c
 
 
bam_plbuf.h
bam_plbuf.h
 
 
bam_plcmd.c
bam_plcmd.c
 
 
bam_quickcheck.c
bam_quickcheck.c
 
 
bam_reheader.c
bam_reheader.c
 
 
bam_rmdup.c
bam_rmdup.c
 
 
bam_rmdupse.c
bam_rmdupse.c
 
 
bam_sort.c
bam_sort.c
 
 
bam_split.c
bam_split.c
 
 
bam_stat.c
bam_stat.c
 
 
bam_tview.c
bam_tview.c
 
 
bam_tview.h
bam_tview.h
 
 
bam_tview_curses.c
bam_tview_curses.c
 
 
bam_tview_html.c
bam_tview_html.c
 
 
bamshuf.c
bamshuf.c
 
 
bamtk.c
bamtk.c
 
 
bedcov.c
bedcov.c
 
 
bedidx.c
bedidx.c
 
 
cut_target.c
cut_target.c
 
 
dict.c
dict.c
 
 
errmod.c
errmod.c
 
 
errmod.h
errmod.h
 
 
faidx.c
faidx.c
 
 
kprobaln.c
kprobaln.c
 
 
kprobaln.h
kprobaln.h
 
 
padding.c
padding.c
 
 
phase.c
phase.c
 
 
sam.c
sam.c
 
 
sam.h
sam.h
 
 
sam_header.c
sam_header.c
 
 
sam_header.h
sam_header.h
 
 
sam_opts.c
sam_opts.c
 
 
sam_opts.h
sam_opts.h
 
 
sam_view.c
sam_view.c
 
 
sample.c
sample.c
 
 
sample.h
sample.h
 
 
samtools.1
samtools.1
 
 
samtools.h
samtools.h
 
 
stats.c
stats.c
 
 
stats_isize.c
stats_isize.c
 
 
stats_isize.h
stats_isize.h
 
 

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samtools

This is the official development repository for samtools.

The original samtools package has been split into three separate but tightly coordinated projects:

  • htslib: C-library for handling high-throughput sequencing data
  • samtools: mpileup and other tools for handling SAM, BAM, CRAM
  • bcftools: calling and other tools for handling VCF, BCF

See also http://github.com/samtools/

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Tools (written in C using htslib) for manipulating next-generation sequencing data

samtools.sourceforge.net/

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  • C 62.6%
  • Roff 16.9%
  • Perl 16.3%
  • Lua 1.9%
  • Makefile 0.9%
  • Java 0.6%
  • Other 0.8%