卸载旧版本samtools

1.  查看samtools版本
$ samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-96b5f2294a
2. 浏览已安装的程序
$ dpkg --list 
3. 卸载程序和所有配置文件
$ sudo apt-get --purge remove samtools
4. 检查samtools是否卸载
$ dpkg --list 

安装版本samtools

# 获取新版本samtools
$ git clone git://github.com/samtools/samtools.git
$ make
config.mk:33: ../htslib/htslib.mk: No such file or directory
config.mk:34: ../htslib/htslib_static.mk: No such file or directory
make: *** No rule to make target `../htslib/htslib_static.mk'.  Stop.

#  安装htslib
$ git clone https://github.com/samtools/htslib.git  
$ autoconf       # Generate the configure script, if needed  
$ ./configure    # Optional, needed for choosing optional functionality  
$ make  
#  报错，需要安装zlib.h和lzma.h
# 安装zlib.h
# $ sudo apt-get install zlib1g-dev
# 安装lzma.h
$ sudo apt-cache search "liblzma"
$ sudo apt-get install liblzma-dev

# 继续安装htslib
$ sudo make install  

# 继续安装samtools
$ ./configure
$ make
$ sudo make install
# 查看samtools版本
$  ./samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.8-20-g4ff8062 (using htslib 1.8-13-g19a66ce)

参考：
如何卸载Ubuntu软件
fatal error: zlib.h & lzma.h : No such file or directory
htslib和Samtool安装步骤