Issues on somatic.pl

[Edison19991109]

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:

 system_call("annotate_variation.pl -geneanno -dbtype refGene -buildver ".$build." ".$output."/".$type."_mutations_".$build.".txt ".$annovar_path.$annovar_db);
  system_call("coding_change.pl --includesnp --alltranscript --newevf ".$output."/".$type."_mutations_".$build.".txt_tmp.txt ".$output."/".$type."_mutations_".$build.".txt".
    ".exonic_variant_function ".$annovar_path.$annovar_db."/".$build."_refGene.txt ".$annovar_path.$annovar_db."/".$build."_refGeneMrna.fa >/dev/null 2>/dev/null");
  system_call("Rscript ".$path."/somatic_script/add_fs_annotation.R ".$output." ".$build." ".$type);
  system_call("rm -f ".$output."/".$type."_mutations_".$build.".txt?*");
}

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?

[tianshilu]

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

[Edison19991109]

Hi @tianshilu ,

Thank you for your help and reply! We have just mistaken flter_vcf.R as equal as filter.R.

Best wishes,
Jianning