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PBTA Histologies: Fusion filtering base (3 of N) #865

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Jan 6, 2021
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PBTA Histologies: Fusion filtering base (3 of N) #865

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bd3a94d
update to use base histologies file
kgaonkar6 Dec 7, 2020
bea7b1d
update to use base histology file
kgaonkar6 Dec 7, 2020
cef95e9
update to use base histology v18
kgaonkar6 Dec 7, 2020
858370f
Update README.md
kgaonkar6 Dec 9, 2020
129c3d3
Update README.md
kgaonkar6 Dec 9, 2020
74b33b5
re-run with udpated pbta-histologies-base.tsv
kgaonkar6 Dec 15, 2020
a3fb859
Merge branch 'fusion_filtering_base' of https://github.com/kgaonkar6/…
kgaonkar6 Dec 15, 2020
a92cd90
Update README.md
kgaonkar6 Dec 17, 2020
c3dfcc9
Update config.yml
kgaonkar6 Dec 17, 2020
c45b630
Update config.yml
kgaonkar6 Dec 17, 2020
318c607
ifelse update re-run
kgaonkar6 Dec 17, 2020
4ad06a0
Merge branch 'fusion_filtering_base' of https://github.com/kgaonkar6/…
kgaonkar6 Dec 17, 2020
bca3e06
Merge branch 'master' into fusion_filtering_base
kgaonkar6 Jan 5, 2021
c4b3101
Merge remote-tracking branch 'upstream/master' into fusion_filtering_…
jaclyn-taroni Jan 6, 2021
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24 changes: 12 additions & 12 deletions analyses/collapse-rnaseq/02-analyze-drops.nb.html
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13 changes: 13 additions & 0 deletions analyses/fusion_filtering/04-project-specific-filtering.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,14 @@ params:
label: "results folder for *tsv files"
value: results
input: string
base_run:
label: "1/0 to run with base histology"
value: 0
input: integer
base_histology:
label: "Base histology file"
value: data/pbta-histologies-base.tsv
input: file
---


Expand Down Expand Up @@ -88,8 +96,13 @@ fusion_calls<-QCGeneFiltered_filtFusion %>% mutate(FusionName=rm_between(.data$F
group<-params$group

# get histology file
if ( params$base_run ==0 ){
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Looks like the only difference here is whether params$base_histology or params$histology is used, so I would reduce your if statement to specify a histology_file variable and then supply that to that code chunk rather than repeating the code chunk twice.

clinical<-read.delim(file.path(root_dir, params$histology), stringsAsFactors = FALSE)
clinical<-clinical[,c("Kids_First_Biospecimen_ID","Kids_First_Participant_ID",group)]
} else {
clinical<-read.delim(file.path(root_dir, params$base_histology), stringsAsFactors = FALSE)
clinical<-clinical[,c("Kids_First_Biospecimen_ID","Kids_First_Participant_ID",group)]
}

# Least number of callers
numCaller<-params$numCaller
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23 changes: 13 additions & 10 deletions analyses/fusion_filtering/04-project-specific-filtering.nb.html
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14 changes: 14 additions & 0 deletions analyses/fusion_filtering/05-QC_putative_onco_fusion_dustribution.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,14 @@ params:
label: "results folder for pbta-fusion-putative-oncogenic.tsv files"
value: results
input: string
base_run:
label: "1/0 to run with base histology"
value: 0
input: integer
base_histology:
label: "Base histology file"
value: data/pbta-histologies-base.tsv
input: file

---

Expand Down Expand Up @@ -69,8 +77,14 @@ fusion_calls<-read_tsv(file.path(root_dir,params$dataPutativeFusion))
outputfolder<-params$outputfolder

#### get histology file
if ( params$base_run ==0 ){
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Same comment here!

clinical<-read_tsv(file.path(root_dir, params$histology), guess_max = 10000) %>%
dplyr::select(Kids_First_Biospecimen_ID, Kids_First_Participant_ID, broad_histology)
} else {
clinical<-read_tsv(file.path(root_dir, params$base_histology), guess_max = 10000) %>%
dplyr::select(Kids_First_Biospecimen_ID, Kids_First_Participant_ID, broad_histology)
}


# add broad_histology to fusion
fusion_calls<-fusion_calls %>%
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51 changes: 29 additions & 22 deletions analyses/fusion_filtering/05-QC_putative_onco_fusion_dustribution.nb.html
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11 changes: 10 additions & 1 deletion analyses/fusion_filtering/README.md
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Expand Up @@ -48,7 +48,16 @@ The code to generate genelistreference.txt and fusionreference.txt is available
* pbta-fusion-recurrently-fused-genes-bysample.tsv

### Run script
`bash run_fusion_merged.sh`
use BASE_SUBTYPING=1 to run this module using the pbta-histologies-base.tsv from data folder while running molecular-subtyping modules for release.
```sh
BASE_SUBTYPING=1 run_fusion_merged.sh
```

OR by default uses pbta-histologies.tsv from data folder
```sh
bash run_fusion_merged.sh
```


#### Order of scripts in analysis
`01-fusion-standardization.R` : Standardizes fusion calls from STARFusion and Arriba
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27,882 changes: 14,147 additions & 13,735 deletions analyses/fusion_filtering/results/FilteredFusion.tsv
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4,026 changes: 2,102 additions & 1,924 deletions analyses/fusion_filtering/results/pbta-fusion-putative-oncogenic.tsv
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5 changes: 2 additions & 3 deletions analyses/fusion_filtering/results/pbta-fusion-recurrent-fusion-byhistology.tsv
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
FusionName broad_histology count
KIAA1549--BRAF Low-grade astrocytic tumor 109
KIAA1549--BRAF Low-grade astrocytic tumor 114
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I'm assuming these results changes are expected, but just going to bring them to attention so we can check.

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yup, these are expected since some samples were updated to Low-grade. More info in Jo Lynne's comment here #865 (comment)

C11orf95--RELA Ependymal tumor 25
EWSR1--FLI1 Mesenchymal non-meningothelial tumor 7
KIAA1549--BRAF Neuronal and mixed neuronal-glial tumor 6
EWSR1--FLI1 Mesenchymal non-meningothelial tumor 5
REV3L--FYN Diffuse astrocytic and oligodendroglial tumor 5
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