ides capp-seq bioinformatics pipeline

Question

[Peter Chung]

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 don't know how to implement the duplex barcode and background polishing packages for the above procedure.

iDES (Integrated Digital Error Suppression): https://cappseq.stanford.edu/ides/download.php#overview

Answer 1

[amjad]

You can try an alternative approach implemented in the ctDNAtools R package:

https://github.com/alkodsi/ctDNAtools

In ctDNAtools, you can use a black list which serves in a way a similar task to the background polishing. The duplex barcode processing needs to be done on your alignment data. You can do something similar with fgbio:

http://fulcrumgenomics.github.io/fgbio/

The Monte Carlo based testing mentioned in the iDES paper is also implemented in ctDNAtools.