The current GATK version is 3.2-2

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Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

edited July 2012

A new tool has been released!

Check out the documentation at MalformedReadFilter.

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• Posts: 9Member
edited September 2012
/usr/java/latest/bin/java -jar /home/hricikt/tools/gatk2_0/gatk2_0.jar -T IndelRealigner -I $bam_files_fullpath -R /home/hricikt/resources/ucsc.hg19.fasta -o$out_file_fullpath -targetIntervals \$interval_files_fullpath -known /home/hricikt/resources/1000G_phase1.indels.hg19.vcf -known /home/hricikt/resources/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MalformedRead

##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: **Duplicate definition of argument with full name: filter_mismatching_base_and_quals**

Post edited by Geraldine_VdAuwera on

Please give some context for the problem you experience, or at least a full stack trace. Also, try without the read filter specified and see if the problem persists.

Geraldine Van der Auwera, PhD

• Posts: 9Member

Running without read filter throws exception for malformed read with mismatching base quality.

##### ERROR ------------------------------------------------------------------------------------------

Is this the full stack trace? Thanks:)

Yes, that's better, thank you. This tells me what version you're using, and since you're using an older version, I can ask you to upgrade to the latest one. This looks like a bug that has been fixed -- but let me know if the problem persists after upgrading.

Geraldine Van der Auwera, PhD

• Posts: 9Member

Got it thanks so much. Do I need to redo RealignerTargetCreator since my .intervals file was generated by the older version? Thanks again:)

You're welcome :)

To be safe I would recommend rerunning the TargetCreator, yes. There shouldn't be much difference if any, but it's better practice.

Geraldine Van der Auwera, PhD

• Posts: 9Member

I've downloaded the most recent version, re-ran RealignerTargetCreator and get the same error when attempting to apply the MalformedReadfilter to IndelRealigner. Leaving out the MalformedReadfilter causes gatk to blow up with execption due to mismatching base quality. I believe this filter worked in v1.6?

##### ERROR ------------------------------------------------------------------------------------------

~

• Posts: 9Member

I'm sorry I forgot to mention that I used the same command from my first post here on Sept 27. Just changed the "gatk2_0" to "gatk2_1"... Thanks.

OK, found the problem. The cmdline argument for this filter was renamed, now you need to call it with either -filterMBQ or --filter_mismatching_base_and_quals. Sorry I didn't catch this one sooner. In future, be sure to check in the docs that you have the right argument name.