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poly-G tail trimming

ecyehecyeh Member
edited February 2019 in Ask the GATK team

As explained by qcfail, illumina's 2-color chemistry, which is used by HiSeq 4000, HiSeq X and NovaSeq, may produce false high-confidence poly-g tail in fastq reads.

Here is my question: is it necessary to do poly-G tail trimming before executing the germline pipelines of GATK?

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