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samtools_0.1.12a.orig.tar.bz2

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/samtools-0.1.12a/bcftools/README

The view command of bcftools calls variants, tests Hardy-Weinberg
equilibrium (HWE), tests allele balances and estimates allele frequency.

This command calls a site as a potential variant if P(ref|D,F) is below
0.9 (controlled by the -p option), where D is data and F is the prior
allele frequency spectrum (AFS).

The view command performs two types of allele balance tests, both based
on Fisher's 
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/samtools-0.1.12a/NEWS

Beta release 0.1.12a (2 December, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is another bug fix release:

 * Fixed a memory violation in mpileup, which causes segfault. Release
   0.1.9 and above are affected.

 * Fixed a memory violation in the indel caller, which does not causes
   segfault, but may potentially affect deletion calls in an unexpected
   way. Release 0.1.10 and above are 
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/samtools-0.1.12a/ChangeLog

------------------------------------------------------------------------
r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h

 * samtools-0.1.10-9 (r844)
 * added the "folded" or reference-free mode for variant calling

---
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/samtools-0.1.12a/AUTHORS

Heng Li from the Sanger Institute wrote most of the initial source codes
of SAMtools and various con
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/samtools-0.1.12a/COPYING

The MIT License

Copyright (c) 2008-2009 Genome Research Ltd.

Permission is hereby granted, free of
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