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Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

read filter for FLAG 0x2 in BAM file

Hi,
I would like to perform base quality score recalibration on only the reads that have the "properly aligned" bit (0x2) set in the FLAG column of the SAM format. Ideally, I would like to use the --read_filter argument. Below is some code that does this to my satisfaction with the PrintReads walker of GATK 2 lite. However, GATK 2 lite does not support base quality score recalibration table creation. Is there any way someone could add the code to the GATK 2 full version?

I am not sure why, but the code seems to only work with the System.out.println() line.

Thanks,
Winni

/*

  • code written by Kiran Garimella
    */

package org.broadinstitute.sting.gatk.filters;

import net.sf.samtools.SAMRecord;

public class ProperPairFilter extends ReadFilter {
@Override
public boolean filterOut(SAMRecord samRecord) {
System.out.println(samRecord.getProperPairFlag());
return !samRecord.getProperPairFlag();
}
}

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