gtc2vcf

Download

$ export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins && bcftools +gtc2vcf
$ export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins && bcftools plugin gtc2vcf
$ bcftools +$BCFTOOLS_PLUGINS/gtc2vcf.so
$ bcftools plugin $BCFTOOLS_PLUGINS/gtc2vcf.so

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Publications

2024

• Pinakhina, D. et al. The effect size of rs521851 in the intron of MAGI2/S-SCAM on HADS-D scores correlates with EAT-26 scores for eating disorders risk. Frontiers in Psychiatry (2024) doi:10.3389/fpsyt.2024.1416009
• Otsuka, I. et al. Increased somatic mosaicism in autosomal and X chromosomes for suicide death. Molecular Psychiatry (2024) doi:10.1038/s41380-024-02718-y
• Haas, D. et al. Early pregnancy associations with Gestational Diabetes: methods and cohort results of the Hoosier Moms Cohort. North American Proceedings in Gynecology & Obstetrics (2024) doi:10.54053/001c.121481
• Patel, W. et al. Role of Transporters and Enzymes in Metabolism and Distribution of 4-Chlorokynurenine (AV-101). Mol. Pharmaceutics (2024) doi:10.1021/acs.molpharmaceut.3c00700

2023

• Locatelli, N. S. et al. Genome assemblies and genetic maps highlight chromosome-scale macrosynteny in Atlantic acroporids. bioRxiv (2023) doi:10.1101/2023.12.22.573044
• Herrick, N., & Walsh. S. ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications. BMC Bioinformatics (2023) doi:10.1186/s12859-023-05548-x
• Babadi, M. et al. GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data. Nature Genetics (2023) doi:10.1038/s41588-023-01449-0
• Kamphuis, P. et al. Clonal Hematopoiesis Defined by Somatic Mutations Infrequently Co-occurs With Mosaic Loss of the Y Chromosome in a Population-based Cohort. Hemasphere (2023) doi:10.1097/HS9.0000000000000956
• Cheng, C. et al. Mosaic Chromosomal Alterations Are Associated With Increased Lung Cancer Risk: Insight From the INTEGRAL-ILCCO Cohort Analysis. Journal of Thoracic Oncology (2023) doi:10.1016/j.jtho.2023.05.001

2022

• Czamara, D. et al. Genome-Wide Copy Number Variant and High-Throughput Transcriptomics Analyses of Placental Tissues Underscore Persisting Child Susceptibility in At-Risk Pregnancies Cleared in Standard Genetic Testing. International Journal of Molecular Sciences (2022) doi:10.3390/ijms231911448
• Babadi, M. et al. GATK-gCNV: A Rare Copy Number Variant Discovery Algorithm and Its Application to Exome Sequencing in the UK Biobank. medRxiv (2022) doi:10.1101/2022.08.25.504851
• Meduri, E. et al. The RNA editing landscape in acute myeloid leukemia reveals associations with disease mutations and clinical outcome. iScience (2022) doi:10.1016/j.isci.2022.105622
• Banes, G. L. et al. Nine out of ten samples were mistakenly switched by The Orang-utan Genome Consortium. Sci Data (2022) doi:10.1038/s41597-022-01602-0
• Qin, N. et al. Association of the interaction between mosaic chromosomal alterations and polygenic risk score with the risk of lung cancer: an array-based case-control association and prospective cohort study. The Lancet Oncology (2022) doi:10.1016/S1470-2045(22)00600-3
• Vasquez Kuntz, K. L. et al. Inheritance of somatic mutations by animal offspring. Genetics (2022) doi:10.1126/sciadv.abn0707
• Uddin, M. et al. Germline genomic and phenomic landscape of clonal hematopoiesis in 323,1121 individuals. medRxiv (2022) doi:10.1101/2022.07.29.22278015
• Hsu, Y. et al. Human rs75776403 polymorphism links differential phenotypic and clinical outcomes to a CLEC18A p.T151M-driven multiomics. Journal of Biomedical Science (2022) doi:10.1186/s12929-022-00822-1
• Eberhardt, R. Y. et al. Detection of mosaic chromosomal alterations in children with severe developmental disorders recruited to the DDD study. bioRxiv (2022) doi:10.1101/2022.03.28.22273024

2021

• Koskela, J. T. et al. Genetic variant in SPDL1 reveals novel mechanism linking pulmonary fibrosis risk and cancer protection. medRxiv (2021) doi:10.1101/2021.05.07.21255988
• Vogel, I. SureTypeSCR: R package for rapid quality control and genotyping of SNP arrays from single cells. F1000Research (2021) doi:10.12688/f1000research.53287.1
• Ainsworth, R. Genetic models to predict the development of colorectal cancer. (2021) doi:10.26021/11897
• Zekavat S., et al. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection. Nat Medicine (2021) doi:10.1038/s41591-021-01371-0
• Sherman, M. A. et al. Large mosaic copy number variations confer autism risk. Nat Neurosci (2021) doi:10.1038/s41593-020-00766-5
• Pini, T. et al. Liquid chromatography-tandem mass spectrometry reveals an active response to DNA damage in human spermatozoa. F&S Science 2, 153-163 (2021) doi:10.1016/j.xfss.2021.03.001

2020

• Kitchen, S. A. et al. STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts. Sci Rep 10, 12488 (2020) doi:10.1038/s41598-020-69101-z
• Kuntz, K. L. V. et al. Juvenile corals inherit mutations acquired during the parent's lifespan. bioRxiv (2020) doi:10.1101/2020.10.19.345538

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