Samtools convert sam to bam

# Basic syntax:
samtools view -S -b sam_file.sam > bam_file.bam
# Where:
#	-S specifies that the input is a sam file
#	-b specified that the output should be written in bam format

# To convert a bam file to a sam file, use:
samtools view -h -o sam_file.sam bam_file.bam

Source: quinlanlab.org

Convert bam to sam samtools

samtools view -h -o yourDir/test.sam test.bam

Source: biostars.org

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