Manipulating SAM and BAM files with samtools

# Get the latest release source files for samtools, unzip, compile and install:

wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2

tar -vxjf samtools-1.9.tar.bz2

cd samtools-1.9

make

sudo make install

# Converting SAM file into BAM file:

samtools view -b -@ [insert number of threads] INPUT.sam -o INPUT.bam

# Sorting BAM files by coordinate

samtools sort -@ [insert number of threads] INPUT.bam -o INPUT_sorted.bam

# Converting SAM file into BAM file sorted by coordinate

samtools sort -@ [insert number of threads] -o INPUT_sorted.bam INPUT.sam