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,
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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