grailbio/conta: Detect cross-contamination

Detect contamination from sequencing data. Input data comes in the format of pileup tsv files. Population minor allele frequency (MAF) is added through a merge with provided dbSNP vcf file. The contamination module builds a baseline error profile across non-SNP alleles and uses this information to calculate the likelihood of each SNP to be contaminated. The contamination level that maximizes the likelihood across all SNPs is reported as the candidate contamination level, along with a call that is made based on the threshold provided, and other related metrics and graphics. Chromosomal regions with loss of heterozygosity (LOH) are not used for contamination analysis.

install.packages("remotes")
remotes::install_github("grailbio/conta")