How do you remove reads from .bam file with FLAG = 0?
I have used the following command to remove alignments with FLAG = 16 from sam file
samtools view -h -F 16 in.bam out.sam
This command does not remove bits with 0...
samtools view -h -F 0 in.bam out.sam
Thoughs??
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Nevermind. After looking at this page I know the identity of 0 and 16 FLAGs are unpaired but mapping reads. You can remove them by this command:
samtools view -h -f 1 in.bam out.sam
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