Dear List Members,
I am hoping that someone might be able to give me a definitive answer as to how rmdup behaves when a bam file contains both paired-end and single-end reads.
This is an extract from the manual:
"samtools rmdup [-sS] <input.srt.bam> <out.bam>
Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads).
OPTIONS:
-s
Remove duplicates for single-end reads. By default, the command works for paired-end reads only.
-S
Treat paired-end reads and single-end reads."
So does this mean that for a bam file containing both single-end and paired-end reads:
rmdup [no option] would remove duplicates for the paired-end reads only?
rmdup -s would remove duplicates for the single-end reads only?
rmdup -S would remove duplicates for both the paired-end and single-end reads?
Or have I misunderstood?
Thanks for any clarification,
Elle
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