genes being excluded from CPSR exploratory track

[MrsLaviniaG]

Hi Sigve

We are supplying a list of genes to CPSR using the _--customlist option. Several of those genes are not making it through to the final CPSR report. Looking at the logs I can see:

2021-02-18 21:31:44 - cpsr-validate-input - WARNING - Ignoring custom-provided gene symbol (ANKRD26) NOT found in CPSR exploratory track 0 2021-02-18 21:31:44 - cpsr-validate-input - WARNING - Choose only symbols from this set: https://github.com/sigven/cpsr/predisposition.md 2021-02-18 21:31:44 - cpsr-validate-input - WARNING - Ignoring custom-provided gene symbol (CSDE1) NOT found in CPSR exploratory track 0 2021-02-18 21:31:44 - cpsr-validate-input - WARNING - Choose only symbols from this set: https://github.com/sigven/cpsr/predisposition.md

https://github.com/sigven/cpsr/predisposition.md does not exist, but https://github.com/sigven/cpsr/blob/master/predisposition.md does. That file does contain ANKRD26, but it does not contain CSDE1. Any insights greatly appreciated!

[sigven]

Hi Lavinia,

Thanks for reaching out. Can you send me the custom list file you are using, I am currently not able to reproduce the error on my side.

thanks, Sigve

[sigven]

One more thing: Do you see ANKRD26 in data/grch38/cpsr_exploratory_track.tsv?

[MrsLaviniaG]

Thanks Sigve for responding so quickly! We may be a version behind your latest update, I will confirm.

[MrsLaviniaG]

Neither of the genes that I mentioned is in the file data/grch38/cpsr_exploratory_track.tsv. Thanks for that, very helpful with troubleshooting. I will update our version and get back to you.

[MrsLaviniaG]

Thanks for your help Sigve, I can see ANKRD26 in the latest version of the data bundle, and I now understand why CSDE1 was omitted.