Number of reads in bam file

How to count the number of mapped reads in a BAM or SAM file?

# get the total number of reads of a BAM file (may include unmapped and duplicated multi-aligned reads)

samtools view -c SAMPLE.bam

568345

# counting only mapped (primary aligned) reads

samtools view -c -F 260 SAMPLE.bam

345623

options

-c count reads and print the total number

-f bitcode output reads that fulfill the checked 'bitcode' criteria, see SAM bitcode fields

-F bitcode exclude reads that match one or more checked 'bitcode' criteria, see SAM bitcode fields

-F 260 output primary aligned mapped reads

read unmapped & not primary alignment criteria 3 & 9 are selected for exclusion

bit 3 + bit 9 = 4 + 256 = 260

http://samtools.sourceforge.net/samtools.shtml

read more

decode SAM bitcode flag number (meaning of flag bits)

http://broadinstitute.github.io/picard/explain-flags.html