I have a bam file which were already sorted (by coordinates) using "samtools sort". However, when I tried to remove duplicate reads using picard's "MarkDuplicates" function, it failed saying that the input bam was not sorted according to the headers. So my questions are the following:
1. Why a bam file sorted by samtools considered not sorted by picard?
2. How can picard tell whether a bam file is sorted or not from the headers?
Thanks for any help on this!
1. Why a bam file sorted by samtools considered not sorted by picard?
2. How can picard tell whether a bam file is sorted or not from the headers?
Thanks for any help on this!
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