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Picard 1.96 - Reads on target

alexsonalexson Member
edited May 2018 in Ask the GATK team

How does Picard 1.96 calculate "reads on target", for example, if only one nucleotide of a read matches a target, does that count as a "read on target"?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I think the tool counts any reads that are mapping within the target intervals. But, which specific tool are you asking about? You may also consider upgrading, as 1.96 is pretty old.


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