BAM file Cheat Sheet - Linux OS

Check tag in bam file:

samtools view -f 4 A02598A4.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam | head

• -f 4 selects reads flagged as unmapped
• If this returns reads → your BAM includes unmapped reads
• If nothing returns → unmapped reads were filtered out before or during BAM generation