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Old 12-29-2011, 10:26 PM   #1
liuxq
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Location: beijing, china

Join Date: Jun 2010
Posts: 36
Default no effect for picard cleansam

Hi all,
I am now using picard v1.58. I want to use CleanSam to soft-clip alignment that hands-off the end of chromosome.

However, I find that the cleansam output bam file has almost no difference with the input bam except adding a @HD line.

What's the problem?

My command is as simply as follows:
java -Xmx4G -jar CleanSam.jar INPUT=SRR305172.bam OUTPUT=SRR305172_cleaned.bam

thanks.
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