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TruSeq Libraries influence in PON
We are trying to build a PON to use with MuTect2 GATK4. Our samples are sequenced using the library TruSeq Nano DNA 350. How important would be that the samples of the PON have exactly the same library? Would be fine if they were sequenced with TruSeq DNA PCR-free or with TruSeq DNA? We are trying to build it using samples from SRA, and there is just one sample from a healthy individual using our configuration (Illumina HiSeq 2x150 TruSeq NanoDNA350).
Thank you very much,
Tamara and Laura