Tagged with #inderealigner
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Created 2015-11-11 20:50:38 | Updated 2015-11-11 20:53:11 | Tags: inderealigner

Comments (6)

Hi GATK,

I'm currently running indelrealigner for tumor and normal paired samples. GATK version is nightly-2015-10-28-gc252559, and the command line is:

java -d64 -Xmx16G -jar /SCRATCH/tools/GenomeAnalysisTK.jar -T IndelRealigner -R reference -I bam.list -known 1kg.indel.vcf -targetIntervals bam_list.intervals --noOriginalAlignmentTags -nWayOut output.map

The error I got is:

ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: No such reader id is available at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$SAMResourcePool.getReaderID(SAMDataSource.java:860) at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.getReaderID(SAMDataSource.java:452) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReaderIDForRead(GenomeAnalysisEngine.java:859) at org.broadinstitute.gatk.engine.io.NWaySAMFileWriter.addAlignment(NWaySAMFileWriter.java:228) at org.broadinstitute.gatk.tools.walkers.indels.ConstrainedMateFixingManager.writeRead(ConstrainedMateFixingManager.java:357) at org.broadinstitute.gatk.tools.walkers.indels.ConstrainedMateFixingManager.addRead(ConstrainedMateFixingManager.java:266) at org.broadinstitute.gatk.tools.walkers.indels.ConstrainedMateFixingManager.addRead(ConstrainedMateFixingManager.java:242) at org.broadinstitute.gatk.tools.walkers.indels.IndelRealigner.emit(IndelRealigner.java:492) at org.broadinstitute.gatk.tools.walkers.indels.IndelRealigner.map(IndelRealigner.java:529) at org.broadinstitute.gatk.tools.walkers.indels.IndelRealigner.map(IndelRealigner.java:148) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version nightly-2015-10-28-gc252559):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: No such reader id is available
ERROR ------------------------------------------------------------------------------------------

I noticed there is another question http://gatkforums.broadinstitute.org/discussion/4621/stack-trace-error-using-indelrealigner You suggest to run picard validatesamfile first. The error I got from there is

"MAPQ should be 0 for unmapped read." Before I fix the mapq problem, I just wanna ask:

  1. Is the mapq the problem? Have you heard this before? What kinds of errors from validatesamfile would possibly cause indelrealigner's failure?
  2. In http://gatkforums.broadinstitute.org/discussion/4621/stack-trace-error-using-indelrealigner, he did realigner across all samples. Would that be the problem? Since it could be possible that I made some mistakes using wrong pair of tumor and normal.

Thank you in advance!


Created 2013-09-18 20:26:06 | Updated | Tags: unifiedgenotyper haplotypecaller indel inderealigner

Comments (4)

I have Ion Torrent data. I am trying to call a variant that I know to exist (confirmed with Sanger). In the position where there is the known indel, I have a depth of roughly 80-90 (in two different runs) and a of those between 20-23% of the reads have the insertion called. What parameters should I be adjusting to get this indel to call? I don't mind a large number of false positives.

I've tried several iterations that include indel realignment using known indels (1000G_phase1 and ills_and_1000G_gold_standard) and also excluding them. I have also tried iterations of setting these flags in UnifiedGenotyper:-stand_call_conf 30.0 -stand_emit_conf 0.0 --min_base_quality_score 0 -glm BOTH --dbsnp dbsnp_137.b37.vcf -nt -rf BadCigar -minIndelCnt 3 -minIndelFrac 0.15. I have also attempted to use HaplotypeCaller: -stand_call_conf 30.0 -stand_emit_conf 0.0 --dbsnp dbsnp_137.b37.vcf -rf BadCigar

Any suggestions would be great.