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99.76% of reads failing DuplicateReadFilter for targetome analysis
I am using GATK HC to identify variants in a target region of about 23kb with very deep sequencing. I get this message during HC that 99.76% of reads failing DuplicateReadFilter. This means that a lot of my reads are being thrown out and hence I am not getting correct variant calls.
First, is GATK HC an appropriate tool to call variants in such a small region with deep sequencing (more than 100X)?
Second, how can I rectify this error of 99% reads failing DuplicateReadFilter?