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# BaseRecalibrator error in a BAM validated with Picard

Member

Hello,

I have a BAM from RNA Seq experiment. The reads are aligned with tophat and then I filtered secondary reads, fixed mate pairs, marked duplicates with picard and realigned with gatk. However, when I try to use BaseRecalibrator function,

-T BaseRecalibrator -nct 12 -R ./SusGenome10v69/Sus_scrofa.Sscrofa10.2.69.dna.toplevel.fa -I ./7_15.corrected.ordered.sremoved.marked.fixed.realigned.fixed.corrected.ordered.sremoved.marked.fixed.realigned.fixed.bam -knownSites ./SusGenome10v69/Sus_scrofa.vcf -o ./7_15.RecalData.grp`

It stops with the error:

##### ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Trying to clip before the start or after the end of a read
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:230) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:218)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

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

The bam file validates properly with the Picard's ValidateSamFile function. I tried with gatk versions, 2.3-9 and 2.4-7 obtaining the same results.

I used the same procedure with other samples without any problem. However, I am unable to recalibrate this sample. I tried to realign the reads with different tophat versions, applied different filters and different procedures, however i am unable to use the BaseRecalibrator function with this sample.

Could you help me?

Thanks!

Tagged:

Hi there,

This sounds like a bug; we'll need to reproduce this error locally. Could you please upload a BAM snippet to our server? Detailed instructions here: http://www.broadinstitute.org/gatk/guide/article?id=1894

Be sure to also upload your reference since you're using a custom one.

• Member

Hi,

I uploaded the requested files in your ftp server (including the reference).

The name of the compressed file is: baseracalibrator.bug.ocanela.tar.gz

Thanks,

• Member

Ok, thank you for the software support!

• Member
edited April 2013

Hi,
Thanks,
Huy

Hi @huyvuong, version 2.5 is not yet available, but you can try the latest nightly build (look on the Downloads page).

• Member

Thank you very much. I tried the latest nightly build and it worked now.

• Member

The version 2.5-2 fixed the problem with my sample.

Thank you for the fix!