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. Author manuscript; available in PMC: 2022 Dec 13.
Published in final edited form as: Cancer Cell. 2021 Nov 4;39(12):1643–1653.e3. doi: 10.1016/j.ccell.2021.10.006

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Critical commercial assays
Ovation Custom Target Enrichment System NuGEN
SureSelect Human All Exon V6 capture kit Illumina
Deposited data
RNA and DNA sequencing data This Paper European Genome-phenome archive
EGAS00001005554
NCI RNA and DNA sequence data Schmitz et al., 2018 dbGaP: phs001444.v2.p1
Software and algorithms
Bcl2fastq https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
STAR2 https://github.com/alexdobin/STAR
SamTools https://sourceforge.net/projects/samtools/
Htseq_count https://htseq.readthedocs.io/en/release_0.11.1/count.html
VarScan2 https://sourceforge.net/projects/varscan/files/
BWA http://bio-bwa.sourceforge.net/
ANNOVAR https://annovar.openbioinformatics.org/en/latest/
SnpEff http://pcingola.github.io/SnpEff/se_introduction/
LymphGen Wright et al. 2020 https://llmpp.nih.gov/lymphgen/index.php