Hi everyone,
I've had a search around and can't find the answer I'm looking for.
I'm wondering if anyone can tell me if it's possible to run Picard MarkDuplicates on a batch of bam files at once? I have 13 bam files in a single directory and would like to remove duplicates from all files and output 13 new bam files with the duplicates removed.
Since this is a java based program I wasn't sure if the same rules applied as running samtools for example on a batch of files from the command line.....
I've had a search around and can't find the answer I'm looking for.
I'm wondering if anyone can tell me if it's possible to run Picard MarkDuplicates on a batch of bam files at once? I have 13 bam files in a single directory and would like to remove duplicates from all files and output 13 new bam files with the duplicates removed.
Since this is a java based program I wasn't sure if the same rules applied as running samtools for example on a batch of files from the command line.....
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