Picard Estimatelibrarycomplexity

Question

[komal.rathi]

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?

Answer 1

[Pierre Lindenbaum]

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