Closed Edison19991109 closed 4 years ago
Hi @Edison19991109 ,
filter.R is for post-processing somatic mutations for a batch of sampels. You could use it for filtering the results of somatic.pl. The detailed instruction of filter.R can be found in READ.md. I also put the instruction here for your convenience.
Thanks! Tianshi
Hi @tianshilu ,
Thank you for your help and reply! We have just mistaken flter_vcf.R as equal as filter.R.
Best wishes, Jianning
Dear @tianshilu ,
Hi! My fellow and I got to know about the QBRC Somatic Pipeline several months ago by a Cell paper discussed in our jounral club, and thanks to your piepline, we have managed to build up a local pipeline in our computer cluster.
However, there are still several code lines in somatic.ql that we could not fully understand. If you would like to help with us, I would highly appreciate it. Thank you in advance!
Here are the issues:
In these code lines, you end up with calling the add_fs_annotation.R. In the home directory, however, we also find a filter.R script. So what is the useage of filter.R? Does it need to be run before calling the add_fs_annotation.R?