Intermediate data on microbiome mix-ups and mixtures

These are intermediate data files for the paper

Lobo AK, Traeger LL, Keller MP, Attie AD, Rey FE, Broman KW (2019) Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice. bioRxiv doi:10.1101/529040

- attieDO_v1.zip - primary genotype data in R/qtl2 format (https://kbroman.org/qtl2)

- calcgenoprob_[chr_range].zip - genotype probability files attieDO_probs[chr].rds (in chunks so that no file is > 5 GB)

- calcgenoprob_maps.zip - genetic and physical maps at which genotype probabilities were calculated (attieDO_gmap.rds and attieDO_pmap.rds)

- imp_snp_RData.zip - imputed genotypes in imp_snp_[chr]_modified.RData, each containing imp_snps (a 500 x no. markers matrix of imputed SNP genotypes, encoded as NA (missing), 1 (AA), 2 (AB), and 3 (BB), plus snpinfo with information on SNP locations

- readcounts.zip - counts of SNP alleles in microbiome reads by sample and chromosome, as sample[sample]_[chr]_readcounts.rds

Also needed is the SQLite database of variants in the Collaborative Cross founders, available at figshare: cc_variants.sqlite doi:10.6084/m9.figshare.5280229.v3

The primary metagenomic sequence data is at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA744213