Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples
Mutation data file loader
Hairpin-structure sequence check function
Homology check function.
BAM file loader
Chromosome number loading function.
Genome loading function.
Analyzing function.
Read check function.
Repeat check function.
Save function.
Mutated position search function.
Summarizing function.
Divide function without 0/0 errors
Clinical sequencing of tumor is usually performed on formalin-fixed and paraffin-embedded 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 micro-homology. Our filtering pipeline focuses on the uneven distribution of the artifacts in each read and removes such errors in formalin-fixed and paraffin-embedded samples without over-eliminating the true mutations detected in fresh frozen samples.