Updated analysis: Fusion Filtering

[kgaonkar6]

What analysis module should be updated and why?

1. During project specific filtering I mistakenly removed "other" fusions while filtering on column Fusion_Type for putative-oncogene fusion list.
2. There is also a spelling mistake in the run_script
3. IGH-@,IGH@ , IGL-@ and IGL@ need to be added to reference list as oncogenic genes.

What changes need to be made? Please provide enough detail for another participant to make the update.

1. During project specific filtering I mistakenly removed "other" fusions while filtering on column Fusion_Type for putative-oncogene fusion list.
   In this chunk:

   OpenPBTA-analysis/analyses/fusion_filtering/04-project-specific-filtering.Rmd

   Line 110 in 87386d2

   ```{r}

   we shouldn't remove dplyr::filter(Fusion_Type != "other") and gather all putative_oncogene fusions at this step.

At this step to scavenge back recurrent inframe/frameshift non-oncogenic fusions use dplyr::filter(Fusion_Type != "other")

OpenPBTA-analysis/analyses/fusion_filtering/04-project-specific-filtering.Rmd

Line 143 in 87386d2

```{r}

2. There is also a spelling mistake in the run_script

   OpenPBTA-analysis/analyses/fusion_filtering/run_fusion_merged.sh

   Line 54 in 87386d2

   Rscript analyses/fusion_filtering/02-fusion-filtering.R --standardFusionFiles $standard_arriba_file,$stranded_starfusion_file \

   
   $stranded_starfusion_file should be $standard_starfusion_file

3. IGH-@,IGH@ , IGL-@ and IGL@ need to be added to reference list as oncogenic genes.

What input data should be used? Which data were used in the version being updated?

v14 version
pbta-fusion-starfusion.tsv.gz
pbta-fusion-arriba.tsv.gz

When do you expect the revised analysis will be completed?

1 day

Who will complete the updated analysis?

@kgaonkar6

[jaclyn-taroni]

We should keep an eye on if this changes the output of fusion-summary (my intuition suggests not, but I'm not sure) and if so, those changes will need to get propagated to: 1) the data download 2) molecular-subtyping-embryonal 3) molecular-subtyping-EPN

[kgaonkar6]

I looked into ^, I reran the fusion-summary analysis and the files seem to be unchanged.

md5sum data/fusion_summary_embryonal_foi.tsv
dd9970e8d64ce7665c6c3983d8d34e98 data/fusion_summary_embryonal_foi.tsv
md5sum analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv
dd9970e8d64ce7665c6c3983d8d34e98 analyses/fusion-summary/results/fusion_summary_embryonal_foi.tsv

md5sum data/fusion_summary_ependymoma_foi.tsv
c93c681aadd9ec3e132bf39379b7053c data/fusion_summary_ependymoma_foi.tsv
md5sum analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv
c93c681aadd9ec3e132bf39379b7053c analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv

[jaclyn-taroni]

Thanks for checking that out @kgaonkar6, looking at your PR (#553) now!

[jaclyn-taroni]

Closed via #553