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  • gatk countcovariate ERROR MESSAGE Read starting with deletion. Cigar: 1D22M1I71M8S

    Hello,

    I received targeted sequence reads from a 454 machine.
    In my way on the application of the GATKV3.0 best practice guideline, I got the following error:

    ##### ERROR MESSAGE: SAM/BAM file SAMFileReader{/tmp/ISDBM229314/ISDBM229314.marked.realigned.fixed.bam} is malformed: Read starting with deletion. Cigar: 1D22M1I71M8S

    I am using bwa0.6.1 hg19 and GATK1.6.2

    Here is the pipeline:
    1/ alignment using bwa bwasw -->sam
    2/ use PICARD AddOrReplaceReadGroups to get an indexed BAM file:
    Code:
    java -Xmx4g -Djava.io.tmpdir=/tmp -jar picard-tools-1.62/AddOrReplaceReadGroups.jar RGID=IDa RGLB=LB RGPL=454 RGPU=pu RGSM=sample SO=coordinate INPUT=sample.sam OUTPUT=sample.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
    3/ GATK MarkDuplicates
    4/ GATK RealignerTargetCreator
    5/ GATK IndelRealigner
    6/ PICARD FixMateInformation
    7/ GATk CountCovariates --> ERROR MESSAGE
    Code:
    java -Xmx4g -jar GATK.jar -l INFO -R h37.fasta -nt 16 -knownSites:dbsnp,VCF dbsnp_135.b37.vcf -I sample.marked.realigned.fixed.bam -T CountCovariates --read_filter BadCigar -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile sample.recal_data.csv
    I have the error with or without the option --read_filter BadCigar

    any ideas? hints? links?
    thank you for your help.
    tuka.

  • #2
    Did you find solution

    Hi aituka,

    I have the sme problem. Were you able to find a solution? If yes, could you share?

    Thanks

    Comment


    • #3
      Our solution is simple: remove the read.

      Comment

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