I am new in bioinformatics. we would like to apply the iDES-enhanced CAPP-Seq (CAncer Personalized Profiling by deep Sequencing), however, I have few questions about the procedures after read those papers. I sincerely wish someone can help me for this.
capp-seq paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016134/
ides capp-seq paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907374/
For capp-seq, the bioinformatics pipeline is from BWA (alignment) -> SAMtools (sort and index) -> custom Perl script for QC (statistics, mapping charactersics, read quality including SAMtools flagstat, FASTQC, BEDtools coverageBED) -> Varscan2 (SNVs/Indels) AND FACTERA (fusions) -> compare allele frequency with paired samples ? (fisher test) -> Seattle (annotation) -> compare ctDNA variants to other ctDNA in the same position ? (fisher test)
I am not sure is it correct, please feel free to comment.
However, for ides capp-seq, I dont know how to implement the duplex barcode and background polishing packages for the above procedure.
iDES (Integrated Digital Error Suppression):