Installing SAMtools on CentOS 7

SAMtools is a suite of programs for interacting with high-throughput sequencing data. SAMTools can be downloaded from

$ cd samtools-1.x # and similarly for bcftools and htslib
$ ./configure --prefix=/where/to/install
$ make
$ make install

In your .bashrc

export PATH=/where/to/install/bin:$PATH # for sh or bash users

Compiling SamTools

Taken from Cufflinks – Getting Started

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

SAMTools (0.1.19)

Step 1: – Download SAMTools

Step 2: – Unpack and compile the SAMTools

# tar -zxvf samtools-0.1.19
# make

Step 3: – Copy the compiled libraries to /usr/local/lib

# cp $SAMTOOLS_HOME/libbam.a /usr/local/lib

Step 4: Copy headers to /usr/local/include

# mkdir /usr/local/include/bam
# cp $SAMTOOLS_HOME/*.h /usr/local/include/bam