Picard Estimatelibrarycomplexity

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

• 3,386 views • link

updated 12.8 years ago by Pierre Lindenbaum

• written 12.8 years ago by komal.rathi

1 answer

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

• 183 views • link

written 12.8 years ago by Pierre Lindenbaum

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