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)