install tabix/bgzip

最新推荐文章于 2023-11-29 09:27:47 发布

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最新推荐文章于 2023-11-29 09:27:47 发布

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原文链接：http://www.cnblogs.com/emanlee/p/4574702.html

本文介绍了如何安装bgzip和tabix，这两个工具分别用于块压缩/解压缩和索引TAB分隔的基因位置文件。主要内容包括下载bcftools和htslib的源代码，然后进行编译和安装。安装完成后，可以使用这些工具处理生物信息学数据。

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bgzip – Block compression/decompression utility

tabix – Generic indexer for TAB-delimited genome position files

SAMtools and BCFtools are distributed as individual packages. The code uses HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

HTSlib is also distributed as a separate package which can be installed if you are writing your own programs against the HTSlib API. HTSlib also provides the bgzip, htsfile, and tabix utilities, so you may also want to build and install HTSlib to get these utilities, or see the additional instructions in INSTALL to install them from a samtools or bcftools source package.

Download current source releases: samtools-1.2 bcftools-1.2 htslib-1.2.1

安装 bcftools 1.2, htslib-1.2.1
wget https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2
tar xvf bcftools-1.2.tar.bz2
cd bcftools-1.2
make
make install
cd htslib-1.2.1
make
make install

使用bgzip，tabix

bgzip -c file.vcf > file.vcf.gz
tabix -p vcf file.vcf.gz

REF:
http://sourceforge.net/projects/samtools/files/tabix/
http://www.htslib.org/doc/tabix.html

https://github.com/samtools/bcftools/releases

http://samtools.github.io/bcftools/bcftools.html

转载于:https://www.cnblogs.com/emanlee/p/4574702.html