https://bioinformaticsonline.com/snippets/view/43965/extract-the-mapped-and-unmapped-reads? https://bioinformaticsonline.com/snippets/view/43965/extract-the-mapped-and-unmapped-reads Fri, 23 Sep 2022 06:18:33 -0500 https://bioinformaticsonline.com/snippets/view/43965/extract-the-mapped-and-unmapped-reads 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]]> Abhi