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Old 11-02-2010, 08:10 AM   #1
louis7781x
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Default Does output-file of bwa-sw contain unmapping reads?

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!!
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Old 04-06-2011, 08:25 AM   #2
wwq413
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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.
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