{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T00:11:57Z","timestamp":1768003917835,"version":"3.49.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: 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\u201330\u00d7) and sample size (20\u201310 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)].<\/jats:p><jats:p>Availability and implementation: AbCD, including its downloadable terminal interface and web-based interface, and the associated tools ShotGun and DesignPlanner, including documentation, examples and executables, are available at http:\/\/www.unc.edu\/\u223cyunmli\/AbCD.html.<\/jats:p><jats:p>Contact: \u00a0yunli@med.unc.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt041","type":"journal-article","created":{"date-parts":[[2013,1,29]],"date-time":"2013-01-29T10:05:32Z","timestamp":1359453932000},"page":"799-801","source":"Crossref","is-referenced-by-count":14,"title":["AbCD: arbitrary coverage design for sequencing-based genetic studies"],"prefix":"10.1093","volume":"29","author":[{"given":"Jian","family":"Kang","sequence":"first","affiliation":[{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kuan-Chieh","family":"Huang","sequence":"additional","affiliation":[{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zheng","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"},{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunfei","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"},{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gon\u00e7alo R.","family":"Abecasis","sequence":"additional","affiliation":[{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yun","family":"Li","sequence":"additional","affiliation":[{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"},{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"},{"name":"1 Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada, 2Department of Biostatistics, 3Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, 4Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 and 5Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7264, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,1,28]]},"reference":[{"key":"2023012810304275100_btt041-B1","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.nbt.2008.12.009","article-title":"Next-generation DNA sequencing techniques","volume":"25","author":"Ansorge","year":"2009","journal-title":"N. Biotechnol."},{"key":"2023012810304275100_btt041-B2","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/nrg3031","article-title":"Exome sequencing as a tool for Mendelian disease gene discovery","volume":"12","author":"Bamshad","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2023012810304275100_btt041-B3","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1101\/gr.100040.109","article-title":"Accurate detection and genotyping of SNPs utilizing population sequencing data","volume":"20","author":"Bansal","year":"2010","journal-title":"Genome Res."},{"key":"2023012810304275100_btt041-B4","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/ncomms1130","article-title":"Deep resequencing reveals excess rare recent variants consistent with explosive population growth","volume":"1","author":"Coventry","year":"2010","journal-title":"Nat. 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