KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
scRNA sequencing data - mouse	Laukoter et al., 2020	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152716
scRNA sequencing data - human HepG2	Hou et al., 2016	GSM2039769 GSM2039770
HepG2 cell line genome data	(Zhou et al., 2019)	ENCODE:ENCBS760ISV
GRCm38.p5	NCBI	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.25/
Ensembl	EMBL-EBI	https://www.ensembl.org/index.html?redirect=no
CA Mouse Genome Project sequencing data	Keane et al., 2011	ftp://ftp-mouse.sanger.ac.uk/current_snps/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz
Supplemental Data Seurat_CountMatrix VCFs HMM_Genotype_Tables Consensus_Trees Dream Challenge	This study	Horwitz, Marshall (2022), “Anderson_LOH_v3”, Mendeley Data, V1, doi: 10.17632/23f7j32zmf.1
Experimental models: organisms/strains
Mouse: CAST/Ei	The Jackson Laboratory	RRID:IMSR_JAX:000928
Mouse: C57BL/6J	The Jackson Laboratory	RRID:IMSR_JAX:00066
Mouse:Emx1-Cre	The Jackson Laboratory	RRID:IMSR_JAX:005628
Software and algorithms
STAR 2.5.0c	Dobin et al., 2013	https://github.com/alexdobin/STAR
Seurat R package	Butler et al., 2018; Stuart et al., 2019	https://satijalab.org/seurat/
GATK	Keane et al., 2011	https://gatk.broadinstitute.org/hc/en-us
HMM R package	Prof. Dr. Lin M. Himmelmann, University of Applied Sciences Rapperswil, Switzerland	https://cran.r-project.org/web/packages/HMM/index.html
MrBayes	Ronquist et al., 2012	http://nbisweden.github.io/MrBayes/
DensiTree	Bouckaert, 2010	https://www.cs.auckland.ac.nz/~remco/DensiTree/
Supplemental Code CSI-scRLA Functions.R GEM_SNPCallerGVCF.sh GEM_RGReOrSortSplit.sh	This study	Horwitz, Marshall (2022), “Anderson_LOH_v3”, Mendeley Data, V1, doi: 10.17632/23f7j32zmf.1