optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants

Shah, Tejas; Liu, J. Z.; Floyd, James A B; Morris, James A.; Wirth, Nicolas T.; Barrett, Jeffrey C.; Anderson, Carl A.

doi:10.1093/bioinformatics/bts180

Cited by 92 publications

(87 citation statements)

References 13 publications

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“…This is obviously imperfect, as genotype calling algorithms for microarrays tend to be unreliable at SNPs with low minor allele counts, even if Illumina's proprietary SNP genotype-calling software GenCall for the Illumina microarrays has been reported to exhibit low error rates (Shah et al, 2012). However, in our comparison, any errors in the Omni1-Quad genotypes will contribute the same impact to the comparison of the different variant callers.…”

Section: Discussionmentioning

confidence: 86%

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

2014

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Motivation: Whole-genome sequencing (WGS) is now routinely used for the detection and identification of genetic variants, particularly single nucleotide polymorphisms (SNPs) in humans, and this has provided valuable new insights into human diversity, population histories and genetic association studies of traits and diseases. However, this relies on accurate detection and genotyping calling of the polymorphisms present in the samples sequenced. To minimize cost, the majority of current WGS studies, including the 1000 Genomes Project (1 KGP) have adopted low coverage sequencing of large number of samples, where such designs have inadvertently influenced the development of variant calling methods on WGS data. Assessment of variant accuracy are usually performed on the same set of low coverage individuals or a smaller number of deeply sequenced individuals. It is thus unclear how these variant calling methods would fare for a dataset of $100 samples from a population not part of the 1 KGP that have been sequenced at various coverage depths. Results: Using down-sampling of the sequencing reads obtained from the Singapore Sequencing Malay Project (SSMP), and a set of SNP calls from the same individuals genotyped on the Illumina Omni1-Quad array, we assessed the sensitivity of SNP detection, accuracy of genotype calls made and variant accuracy for six commonly used variant calling methods of GATK, SAMtools, Consensus Assessment of Sequence and Variation (CASAVA), VarScan, glfTools and SOAPsnp. The results indicate that at 5Â coverage depth, the multisample callers of GATK and SAMtools yield the best accuracy particularly if the study samples are called together with a large number of individuals such as those from 1000 Genomes Project. If study samples are sequenced at a high coverage depth such as 30Â, CASAVA has the highest variant accuracy as compared with the other variant callers assessed.

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Section: Discussionmentioning

confidence: 86%

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

2014

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“…S2). We also compared our method with optiCall (Shah et al, 2012) and found for 10 705 singletons, the SWC of optiCall was 98.21% versus 99.27% for zCall ( Supplementary Fig. S3).…”

Section: Resultsmentioning

confidence: 99%

zCall: a rare variant caller for array-based genotyping

et al. 2012

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Summary: zCall is a variant caller specifically designed for calling rare single-nucleotide polymorphisms from array-based technology. This caller is implemented as a post-processing step after a default calling algorithm has been applied. The algorithm uses the intensity profile of the common allele homozygote cluster to define the location of the other two genotype clusters. We demonstrate improved detection of rare alleles when applying zCall to samples that have both Illumina Infinium HumanExome BeadChip and exome sequencing data available.

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“…Clustering of the intensities and genotype calling was performed using the optiCall clustering program, with a no-calling cutoff set to 0.7. 27 To avoid false positive signals in the genome-wide association studies analysis, a stringent quality control (QC) was performed using PLINK software version 1.07. 28 …”

Section: Genetic Analysismentioning

confidence: 99%

Identification of Clinical and Genetic Parameters Associated with Hidradenitis Suppurativa in Inflammatory Bowel Disease

Janse¹,

Koldijk²,

Spekhorst

et al. 2016

Inflammatory Bowel Diseases

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HS is present in 6.8% to 10.6% of IBD patients. Co-morbid HS is associated with an early onset of IBD in which anti-tumor necrosis factor-α therapy and surgical resections are often needed. We identified a suggestive protective association with ELOVL7 and suggestive risk association with the genes SULT1B1 and SULT1E1 for HS, in the context of IBD. These genetic associations need further exploration and replication in additional independent cohorts.

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optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants

Cited by 92 publications

References 13 publications

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

zCall: a rare variant caller for array-based genotyping

Identification of Clinical and Genetic Parameters Associated with Hidradenitis Suppurativa in Inflammatory Bowel Disease

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