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Extract the mapped and unmapped reads !
By Abhinav 583 days ago
PROCESSORS=20
#Single_End_Layout:
samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam
samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapped.bam
#Paired_End_Layout
samtools view --threads $PROCESSORS -b -f 2 in.bam > mapped.bam
samtools view --threads $PROCESSORS -b -F 2 in.bam > unmapped.bam
