Open MareikeJaniak opened 4 weeks ago
Thanks a lot, Mareike! Never be sorry for filing issues, these are very useful. I think you identified what needs to be fixed, I'll just try to reproduce it first, and make a patch for it. And such bugs clearly hints to some more robust testing procedures before moving to release. ;-) . Anyways, I'll make a fix, prob next week, also working on some other upgrades (CNA plot, germline integration etc).
Thanks again!
best, Sigve
Hi Mareike,
I've re-run your sample with the upcoming version (2.1.0, also with updated reference data):
Results availabe here: https://www.dropbox.com/scl/fo/12ocw7d70by3w9c3fgx37/AExdqvjAVwWTuwp18txMv68?rlkey=5uvhcucz5og98xrwhuqs8nclq&dl=0
Sorry for the delay:)
best, Sigve
Hi Sigve,
Thanks for the update and for all of the updates in the upcoming version! We're looking forward to testing it out.
Best, Mareike
Hi,
Apologies for opening yet another issue, but I've encountered a small error with pcgr. I believe this is related to our test dataset, which is limited to chromosome 19, and the way that R reads in numeric columns. When using the --vcf2maf flag in the command, the following error occurs:
I think this might be happening because the Chromosome column in this case only contains "19", which is leading R to read this column in as numeric, instead of as a character. I realize this is a bit of a niche issue, but others may come across it if their datasets don't contain data on chr X and Y.
I'm using pcgr v2.0.3 with the following command:
The same command runs fine with the example data and it also finishes successfully with our test dataset if I omit the
--vcf2maf
flag. I'm attaching the input file used here. HCC1395.hc.vt.annot.flt.vcf.gzBest, Mareike