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It would be great if we can extract duplicated reads and check where they fall on the genome.
Since they're flagged in the BAM file, this isn't too hard. I use samtools for tasks like this: samtools view -f 0x400 -b -o Sample_dupes.bam Sample.bam
samtools view -f 0x400 -b -o Sample_dupes.bam Sample.bam
Ah, that's a good idea. Much simpler than writing a new read filter
Geraldine Van der Auwera, PhD