Retaining secondary and supplementary alignments

[calcasey]

Hi,

I am working with RNA-seq data to identify gene fusions. I'm currently using fgbio for UMI grouping and consensus sequence calling.

As well as using the tools in the latest fgbio release to process the UMIs, I would like to test an adapted version of GroupReadsByUmi which does not filter out secondary and supplementary alignments, to see how this affects the fusion calling results.

However, I am new to scala and sbt, and I am unsure how to build an executable JAR file to test the adapted tool.

I have removed this line in fgbio-2.1.0/src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala:

.filter(r => !r.secondary && !r.supplementary)

which I am hoping will do the trick. I would be very grateful if you could advise me on how to build an executable JAR file so I can test this out. I noticed README.md mentions sbt assembly, but do I need to edit build.sbt before running this?

Additionally, I would appreciate your opinion on what unintended negative consequences I might run into downstream in my analysis if I retain secondary and/or supplementary alignments, or whether it might be better to retain only one or the other. I am also fairly new to fusion calling, so I am not sure whether the benefits of retaining secondary and/or supplementary alignments for identifying fusion breakpoints outweigh the disadvantages of retaining potential alignment artifacts.

Thank you!

[nh13]

See this link for how to build: https://github.com/fulcrumgenomics/fgbio#building.

I'll leave this issue open in the case we have time in the future to answer your additional questions. My apologies as we are prioritized paid client work at this time.

[calcasey]

Thank you very much!