CHARR efficiently estimates contamination from DNA sequencing data.DNA sample contamination is a major issue in clinical and research applications of whole genome and exome sequencing.  We propose a new metric to estimate DNA sample contamination from variant-level whole genome and exome sequence data, CHARR, Contamination from Homozygous Alternate Reference Reads, which leverages the infiltration of reference reads within homozygous alternate variant calls.  CHARR uses a small proportion of variant-level genotype information and thus can be computed from single-sample gVCFs or callsets in VCF or BCF formats, as well as efficiently stored variant calls in Hail VDS format.  Our results demonstrate that CHARR accurately recapitulates results from existing tools with substantially reduced costs, improving the accuracy and efficiency of downstream analyses of ultra-large whole genome and exome sequencing datasets.
CHARR
CHARR efficiently estimates contamination from DNA sequencing data.DNA sample contamination is a major issue in clinical and research applications of whole genome and exome sequencing.  We propose a new metric to estimate DNA sample contamination from variant-level whole genome and exome sequence data, CHARR, Contamination from Homozygous Alternate Reference Reads, which leverages the infiltration of reference reads within homozygous alternate variant calls.  CHARR uses a small proportion of variant-level genotype information and thus can be computed from single-sample gVCFs or callsets in VCF or BCF formats, as well as efficiently stored variant calls in Hail VDS format.  Our results demonstrate that CHARR accurately recapitulates results from existing tools with substantially reduced costs, improving the accuracy and efficiency of downstream analyses of ultra-large whole genome and exome sequencing datasets.
CHARR
CHARR efficiently estimates contamination from DNA sequencing data.DNA sample contamination is a major issue in clinical and research applications of whole genome and exome sequencing.  We propose a new metric to estimate DNA sample contamination from variant-level whole genome and exome sequence data, CHARR, Contamination from Homozygous Alternate Reference Reads, which leverages the infiltration of reference reads within homozygous alternate variant calls.  CHARR uses a small proportion of variant-level genotype information and thus can be computed from single-sample gVCFs or callsets in VCF or BCF formats, as well as efficiently stored variant calls in Hail VDS format.  Our results demonstrate that CHARR accurately recapitulates results from existing tools with substantially reduced costs, improving the accuracy and efficiency of downstream analyses of ultra-large whole genome and exome sequencing datasets.
CHARR