Find Total, Mapped, and Unmapped Alignments in a BAM File

Often one of the first descriptive statistics of interest for a .bam file is the total number of alignments included in the BAM file.  An alignment is where a read from a next-generation sequencing approach maps to the reference genome.  There are a few ways of calculating the total number of mapped, unmapped, and overall number of alignments, but in my opinion samtools provides the most powerful and efficient means of doing this.  Here are some simple example scripts to count total alignments and total reads in a bam file.

	###########################
	# Using samtools idxstats # # quickest approach
	###########################
	# Total Alignments
	samtools idxstats filename.bam | awk '{s+=$3+$4} END {print s}'
	# Mapped Alignments
	samtools idxstats filename.bam | awk '{s+=$3} END {print s}'
	# Unmapped Alignments
	samtools idxstats filename.bam | awk '{s+=$4} END {print s}'
	#######################
	# Using samtools view # # more options
	#######################
	# Total Alignments
	samtools view -c filename.bam
	# Mapped Alignments
	samtools view -c -F 4 filename.bam
	# Unmapped Alignments
	samtools view -c -f 4 filename.bam
	# Mapped Alignment and its Mate Mapped
	samtools view -c -f 1 -F 12 filename.bam
	# Total Reads
	samtools view filename.bam | cut -f 1 | sort | uniq | wc -l

view raw total alignments.sh hosted with ❤ by GitHub