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Old 04-13-2012, 02:37 PM   #1
lyz1030
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Default About Picard and SAM-JDK

Hi,

I have a question about SAM-JDK. In the class 'net.sf.samtools.SAMRecord', what is the meaning of the method getReadPairedFlag() and getProperPairFlag(). If getReadPairedFlag() returns ture and getProperPairFlag() return false, what does this SAMRecord stand for? I want to know if this SAMRecord should be used for variant calling?

Thanks,
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Old 04-13-2012, 05:31 PM   #2
swbarnes2
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"proper pairs" means that whatever software made your .bam record thinks that the reads are in the right orientation with respect to each other, and have the right distance between them, so set the flag value 2 to show this. The paired flag just means that the software making the .bam was told it was dealing with paired data, so it set the 1 flag.

You have to decide for yourself what an improperly paired set of reads means in the context of your experiment.
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Old 04-13-2012, 10:12 PM   #3
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Quote:
Originally Posted by swbarnes2 View Post
You have to decide for yourself what an improperly paired set of reads means in the context of your experiment.
Refer to the software manual of the software that created the SAM/BAM.
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