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Fig. 1 | Genome Medicine

Fig. 1

From: Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches

Fig. 1

Comparing genotype sketches to compute relatedness measures for pairs of samples. a Observed counts for the reference (Ref.) and alternate (Alt.) allele at each of the tested 17,766 loci are converted into genotypes (see main text for details) to create a “sketch” for each sample. b The genotypes for each sample are then converted into three bit vectors: one for homozygous reference (HOMREF) genotypes, one for heterozygous (HET) genotypes, and one for homozygous alternate (HOMALT) genotypes. The length of each vector is the total number of autosomal variants in the sketch (i.e., 17,384) divided by 64, and the value for each bit is set to 1 if the sample has the particular genotype at the given variant site. For example, four variant sites are shown in b and the hypothetical individual has a homozygous alternate genotype for the second variant (the corresponding bit is set to 1), but is not homozygous for the alternate allele at the other three variant sites (the corresponding bits are set to 0). c The bit vectors for a pair of samples can be easily compared to calculate relatedness measures such as identity-by-state zero (IBS0, where zero alleles are shared between two samples) through efficient, bitwise operations on the bit arrays for the relevant genotypes

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