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Markduplicate error on gatk4
Dear All . I use samtools (1.6) for merge bam file and then I run markduplicate. I have this error:
Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 1: 432_L002:B0P8DQ1:88:CA2D7ACXX:2:2314:7568:79248
I use this command:
picard MarkDuplicates I=mapped_reads/bam/432_sortedR.bam O=mapped_reads/merged_samples/432.dedup.bam M=mapped_reads/merged_samples/432.dup.metrics.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT
Any idea how to resolve? with markduplicate from gatk3.8 I don't have this errror