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compare tools for SNV, Indels, SV, EC-DNA vs GDC pipeline #30

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kelly-sovacool opened this issue Feb 6, 2024 · 2 comments

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kelly-sovacool commented Feb 6, 2024 •

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GDC: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/

features we'd like to support: snv, indel, structural variants, extra chromosomal dna
create table of tools that support above features
for each, are we DIYing consensus calling?

kelly-sovacool changed the title ~~compare tools for SNV, Indels, SV, EC-DNA~~ compare tools for SNV, Indels, SV, EC-DNA vs GDC pipeline

kelly-sovacool self-assigned this

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kelly-sovacool commented Feb 8, 2024 •

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Also compare to KFDRC somatic workflow https://github.com/kids-first/kf-somatic-workflow

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kelly-sovacool commented Feb 9, 2024 •

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Somatic Variant Callers

Adapted from https://github.com/kids-first/kf-somatic-workflow?tab=readme-ov-file#somatic-variant-workflow-callers

Caller	CNV	SNV	SV	ecDNA	indel	-	KFDRC	NCI GDC	LOGAN	XAVIER
AmpliconArchitect				x			x		?	?
CNVkit	x						x		?	?
Control-FREEC	x						x		?	?
GATK CNV	x						x	?	?	?
Lancet		x					x		?	?
Manta			x		?		x		?	?
Mutect2		x			x		x	x	?	?
Strelka2		x					x		?	?
THeTa2			x		?		x		?	?
VarDict		x					x		?	?
MuSE		x						x	?	?
VarScan2	x	x			x			x	?	?
Pindel					x			x	?	?
BRASS			x					x	?	?
CaVEMan		x						x	?	?
AscatNGS	x							x	?	?

Legend

CNV - copy number variant
SNV - single nucleotide variant
SV - structural variant
ecDNA - extra chromosomal DNA
indel - insertion/deletion

kelly-sovacool added this to the 2024-02 milestone

kelly-sovacool modified the milestones: 2024-02, 2024-03

kelly-sovacool removed this from the 2024-03 milestone

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