read filter for FLAG 0x2 in BAM file

wkretzsch

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(); } }

Geraldine_VdAuwera

Indeed -- although it would be more accurate to say source code of 2.4, since past versions will remain closed. (minor quibble just to be entirely clear)

wkretzsch

scratch that, this code works fine as well:

/* * 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) { return !samRecord.getProperPairFlag(); } }

wkretzsch

It looks like this will become a non-issue with the opening of the source code of GATK 2.0.