Does output-file of bwa-sw contain unmapping reads?

[louis7781x]

Hello everyone,I want to know when we use bwa-sw to alignment,Does its output.sam contain "non-mapping reads"? Because I use default to align 454 against human genomes,output.sam using samtools transfer to bam;and use the command "samtool view f -4 <output.bam>" . It doesn't show any non-mapping reads.

If anyone know the answer,please let me know!!

thanks!!!

Best regard!!

[wwq413]

f -4 means filter unmapped reads and keep the mapped reads which are with flag 0 or 16.
Since you filter the output, you couldn't see any unmapped reads.