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.bam568345 # counting only mapped (primary aligned) reads samtools view -c -F 260 SAMPLE.bam345623 options -c count reads and print the total number -f bitcode only output reads with all bits in 'bitcode' present in the FLAG field -F bitcode skip reads with bits present in 'bitcode' -F 260 only output reads that are not unmapped (flag 4 is not set) and only primary alignment (flag 256 is not set)http://samtools.sourceforge.net/samtools.shtml decode SAM flag field (meaning of flag bits) http://broadinstitute.github.io/picard/explain-flags.html |