Can anyone tell me how to remove reads whose mate does not map as expected? I know GATK is able to do this.
There is an option fixmate in samtools, but it could not be used to remove the reads I described above.
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devinliao0918 •
I might be wrong here, but looking at the sam flags;
2 - for read mapped in proper pair
So you can just keep the reads mapped in proper pair.
samtools view -f 2 foo.bam
Does this mean that I have to convert the Bam file into sam file first? I wonder whether there is a way to remove reads unmapped in proper pair.
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