Variant Calling Metrics

Metrics, similar to the metrics computed by RTG vcfstats, are reported on a per sample level. Metrics are reported for each sample in multi sample VCF and gVCFs. Based on the run, case metrics are reported as either standard VARIANT CALLER or JOINT CALLER. Metrics are reported both for the raw (PREFILTER) and hard filtered (POSTFILTER) VCFs.

•

Number of samples—The number of samples in the population/ joint VCF.

•

Reads Processed—The number of reads used for variant calling, which excludes any duplicate marked reads and reads falling outside of the target region.

•

Total—The total number of variants (SNPs + MNPs + indels).

•

Biallelic—The umber of loci that do not contain two observed alleles.

•

Multiallelic—The number of loci that do not contain three or more observed alleles

•

SNPs—A variant is counted as an SNP when the reference, allele 1, and allele 2 are all of length 1.

•

MNPs—A variant is counted as an MNP when the reference, allele 1, and allele 2 are all an equal length other than 1.

•

Indels—Every other variant side is considered an Indel. For example, if allele 1 is of length 1, but allele 2 is not, then the variant site is classified as an Indel.

•

(Chr X SNPs)/(Chr Y SNPs) ratio in the genome (or the target region)—The number of SNPs in chromosome X (or in the intersection of chromosome X with the target region) divided by the number of SNPs in chromosome Y (or in the intersection of chromosome Y with the target region). If there was no alignment to either chromosome X or chromosome Y, this metric is shown as not applicable.

•

SNP Transitions—An interchange of two purines (A↔G) or two pyrimidines (C↔T).

•

SNP Transversions—Interchange of purine and pyrimidine bases Ti/Tv ratio. The ratio of transitions to transitions.

•

Heterozygous—The number of heterozygous variants.

•

Homozygous—The number of homozygous variants.

•

Het/Hom ratio—Heterozygous/ homozygous ratio.

•

In dbSNP—The number of variants detected that are present in the dbSNP reference file.

•

Novel—The total number of variants, ie, the number of variants in dbSNP.