AUDACITY

AUDACITY is novel computational approach for the identification of Runs of Homozygosity by using VCF files from whole-exome and whole-genome sequencing data generated by second generation sequencing technologies.
AUDACITY is a tool integrating novel RoH detection algorithm and autozygosity prediction score for prioritization of mutation-surrounding regions.

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The AUDACITY tool has been published on Computational and Structural Biotechnology Journal (CSBJ).
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You can find it at https://www.sciencedirect.com/science/article/pii/S2001037020303354
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AUDACITY workflow. Panel a: AUDACITY takes as input genotype data in VCF file format and follows 4 analysis steps for RoH identification by DIDOH3M2 (Genotype Extraction, Hidden Markov Model, Viterbi algorithm) and classification by RLOD (Score calculation). For this latter step, AUDACITY can exploit allele frequencies by 1K Genome Project Phase 3 as well as calculate custom allele frequencies from genotypes in the input VCF file. Panel b: The Hidden Markov Model is the core of the DIDOH3M2 algorithm leading to RoH identification. Panel c: RLOD allows to classify ROH based on the allele frequencies of SNP genotypes forming the RoH diplotype.

Genomic patterns of homozygosity in 6 human populations. a Gaussian kernel density estimates of the ROH size distribution in each of the 6 populations (YRI, BEB, CEU, JPT, CLM and FIN). b Mean of each ROH class (A, B and C) and the boundaries between classes A and B and classes B and C for each of the 6 populations. Dotted lines define the limits of class A (small) ROHs, continuous lines define the limits of class B (medium) ROH and dashed lines define the limits of class C (Large) ROH. Filled circles represents the mean size of class A ROH, filled squares the mean size of Class B ROH and filled rhombus the mean size of Class C ROH. c?f Distribution of total ROH lengths over all individuals in each of the 6 populations, for all three classes combined ( c ), for class A ( d ), for class B ( e ) and for class C ( f ). Data are shown as violin plots: each violin contains a vertical black line (25?75% range) and a horizontal white line (median). g-j report the Pairwise comparison of per-Individual Total ROH Lengths across Size Classes. A vs B (g), A vs C (h) and B vs C (i).

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