Question: picard CollectInsertSizeMetrics error
gravatar for sunnykevin97
4 months ago by
sunnykevin9710 wrote:

Hi, why Im getting the error message using picard insert-metrics only on some bam files ?

xception in thread "main" htsjdk.samtools.SAMFormatException: **SAM validation error: WARNING: Read name D00360:95:H2YWMBCXX:1:2113:8832:19449, No M or N operator between pair of D operators in CIGAR**
    at htsjdk.samtools.SAMUtils.processValidationErrors(
    at htsjdk.samtools.BAMRecord.getCigar(
    at htsjdk.samtools.SAMRecord.getAlignmentEnd(
    at htsjdk.samtools.SAMRecord.computeIndexingBin(
    at htsjdk.samtools.SAMRecord.isValid(
    at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(
    at htsjdk.samtools.BAMFileReader$
    at htsjdk.samtools.BAMFileReader$
    at htsjdk.samtools.SamReader$
    at htsjdk.samtools.SamReader$
    at picard.analysis.SinglePassSamProgram.makeItSo(
    at picard.analysis.SinglePassSamProgram.doWork(
    at picard.cmdline.CommandLineProgram.instanceMain(
    at picard.cmdline.PicardCommandLine.instanceMain(
    at picard.cmdline.PicardCommandLine.main(
alignment assembly genome • 200 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by sunnykevin9710
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:


ADD COMMENTlink modified 4 months ago by RamRS20k • written 4 months ago by Pierre Lindenbaum116k
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