Sequence Error Filtering Pipeline for FFPE Samples

Clinical sequencing of tumor is usually performed on formalin-fixed and paraffin-embedded (FFPE) samples and have many sequencing errors. We found that the majority of these errors are detected in chimeric read caused by single-strand DNA with microhomology. Our filtering pipeline focuses on the uneven distribution of the artifacts in each read and removes such errors in FFPE samples without over-eliminating the true mutations detected in fresh frozen samples.


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