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Old 02-15-2011, 02:00 PM   #1
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Default Read Duplicates

I used picard tools to mark the duplicates in .bam file. But I want to know more about those duplicates in .bam file. For example, what is the frequency distribution of duplicates with different length? Is there any easy way to do that? Is there any tools can walk through .bam/.sam file to get that information?

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Old 02-15-2011, 07:17 PM   #2
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this may help you:

rmdup samtools rmdup [-sS] <> <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).

-s Remove duplicate for single-end reads. By default, the command works for paired-end reads only.
-S Treat paired-end reads and single-end reads.
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