Illumina/interop

interop-summary: description of columns

nick-youngblut opened this issue · 2 comments

It would be helpful if https://illumina.github.io/interop/summary_table.html (and/or the summary cli help docs) included a description of the columns.

For instance, is Reads PF actually % Pass Filter as in

* Lane,Tile,Cycle,Read,Cycle Within Read,Density(k/mm2),Density Pf(k/mm2),Cluster Count (k),Cluster Count Pf (k),% Pass Filter,% Aligned,% Phasing,% Prephasing,Error Rate,%>= Q20,%>= Q30,P90|A,P90|C,P90|G,P90|T,% No Calls,% Base|A,% Base|C,% Base|G,% Base|T,Fwhm|A,Fwhm|C,Fwhm|G,Fwhm|T,Corrected|A,Corrected|C,Corrected|G,Corrected|T,Called|A,Called|C,Called|G,Called|T,Signal To Noise,Time,Surface,Swath,Tile Number
?

The same goes for other columns such as whether Density k/mm^2, as in

* Lane,Tile,Cycle,Read,Cycle Within Read,Density(k/mm2),Density Pf(k/mm2),Cluster Count (k),Cluster Count Pf (k),% Pass Filter,% Aligned,% Phasing,% Prephasing,Error Rate,%>= Q20,%>= Q30,P90|A,P90|C,P90|G,P90|T,% No Calls,% Base|A,% Base|C,% Base|G,% Base|T,Fwhm|A,Fwhm|C,Fwhm|G,Fwhm|T,Corrected|A,Corrected|C,Corrected|G,Corrected|T,Called|A,Called|C,Called|G,Called|T,Signal To Noise,Time,Surface,Swath,Tile Number
?

InterOp provides all the metrics for Sequencing Analysis Viewer (SAV). The SAV documentation has the description for each metric and can be found here:
https://support-docs.illumina.com/SW/SAV/Content/SW/SAV/Metrics.htm

Thanks @ezralanglois ! Maybe it would be helpful to include a link to the metrics page at https://illumina.github.io/interop/summary_table.html?