Question: Picard Estimatelibrarycomplexity
gravatar for komal.rathi
6.1 years ago by
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.5k wrote:

I am trying to run EstimateLibraryComplexity.jar on a BAM file obtained from GSNAP:

java -jar EstimateLibraryComplexity.jar INPUT=/home/krathi/Downloads/C00060_filter_sort.bam OUTPUT=output

but I am getting this error:

Exception in thread "main" net.sf.samtools.SAMFormatException: SAM validation error: WARNING: Read name HWI-ST1006:108:D245BACXX:6:1313:13615:41054, No M or N operator between pair of D operators in CIGAR

My BAM file is filtered & sorted. What is going wrong?

picard • 2.2k views
ADD COMMENTlink modified 6.1 years ago by Pierre Lindenbaum124k • written 6.1 years ago by komal.rathi3.5k
gravatar for Pierre Lindenbaum
6.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

Picard validation errors may be turned into warnings by passing the command line argument VALIDATION_STRINGENCY=LENIENT.

ADD COMMENTlink written 6.1 years ago by Pierre Lindenbaum124k
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