#959 Lgat update hotspots

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Rerun LGAT subtyping with hotspot+consensus maf

What was your approach?

Just add hotspot maf pbta-snv-scavenged-hotspots.maf.tsv.gz from hotspot-detection to the snv calls used for subtyping.

What GitHub issue does your pull request address?

959

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

NA

Is there anything that you want to discuss further?

I didn't expect any rna samples update I think the changes got in here : https://github.com/AlexsLemonade/OpenPBTA-analysis/commit/a73f44025eaf4cc07e562685e147f0e5ddacaba3#diff-bc6801a8061034d6b8f1ee90ed5771b19185f2f03276e0760cfa181f226da626 seems to have removed BS_J6VKB1VE ( 7316-974 ) from lgat samples but I don't see description why the sample was removed in that PR.

The sample has pathology_diagnosis == "Low-grade glioma/astrocytoma (WHO grade I/II)" so should be added to the lgat fusion sample list.

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

tables

What is your summary of the results?

2 sample have been updated because of adding hotspot mafs 7316-2575 and 7316-32

	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	IMPACT	Tumor_Sample_Barcode	Hugo_Symbol	HGVSp_Short	SIFT	DOMAINS	caller
1	chr7	140781602	140781602	+	Missense_Mutation	MODERATE	BS_V3ZNXRHK	BRAF	p.G469A	deleterious(0.01)	cd14062,Gene3D:3.30.200.20,Pfam_domain:PF07714,SMART_domains:SM00220,Superfamily_domains:SSF56112,PROSITE_profiles:PS50011,hmmpanther:PTHR44000:SF3,hmmpanther:PTHR44000,PROSITE_patterns:PS00107	mutect2;strelka2;vardict
2	chr7	140753327	140753336	+	Frame_Shift_Del	HIGH	BS_F969DNHD	BRAF	p.V600Dfs*47	.	cd14062,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112,PROSITE_profiles:PS50011,hmmpanther:PTHR44000:SF3,hmmpanther:PTHR44000	lancet
3	chr7	140753322	140753323	+	Frame_Shift_Ins	HIGH	BS_F969DNHD	BRAF	p.S605Efs*7	.	cd14062,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112,PROSITE_profiles:PS50011,hmmpanther:PTHR44000:SF3,hmmpanther:PTHR44000	lancet

Reproducibility Checklist

• [x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [x] This analysis has been added to continuous integration.

Documentation Checklist

• [x] This analysis module has a README and it is up to date.
• [x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [x] The analytical code is documented and contains comments.

[kgaonkar6]

Thanks for the review! The fusion file shows that BS_J6VKB1VE was added in this PR because it seems to have been removed in a73f440.