AbCD: arbitrary coverage design for sequencing-based genetic studies.
Recent advances in sequencing technologies have revolutionized genetic studies. Although high-coverage sequencing can uncover most variants present in the sequenced sample, low-coverage sequencing is appealing for its cost effectiveness. Here, we present AbCD (arbitrary coverage design) to aid the design of sequencing-based studies. AbCD is a user-friendly interface providing pre-estimated effective sample sizes, specific to each minor allele frequency category, for designs with arbitrary coverage (0.5-30×) and sample size (20-10 000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans). In addition, we also present two software tools: ShotGun and DesignPlanner, which were used to generate the estimates behind AbCD. ShotGun is a flexible short-read simulator for arbitrary user-specified read length and average depth, allowing cycle-specific sequencing error rates and realistic read depth distributions. DesignPlanner is a full pipeline that uses ShotGun to generate sequence data and performs initial SNP discovery, uses our previously presented linkage disequilibrium-aware method to call genotypes, and, finally, provides minor allele frequency-specific effective sample sizes. ShotGun plus DesignPlanner can accommodate effective sample size estimate for any combination of high-depth and low-depth data (for example, whole-genome low-depth plus exonic high-depth) or combination of sequence and genotype data [for example, whole-exome sequencing plus genotyping from existing Genomewide Association Study (GWAS)].
Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada.
Jian
J
Kang
Kuan-Chieh
KC
Huang
Zheng
Z
Xu
Yunfei
Y
Wang
Gonçalo R
GR
Abecasis
Yun
Y
Li
D005787:Gene Frequency; D023281:Genomics; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software