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demuxlet specifications

Information


Unique identifier OMICS_23585
Name demuxlet
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A file produced by the standard 10x sequencing platform or any other barcoded single cell RNA-seq (with proper --tag-UMI and --tag-group) options, a VCF/BCF file containing the genotype (GT), posterior probability (GP), or genotype likelihood (GL) to assign each barcode to a specific sample (or a pair of samples).
Input format SAM,BAM,CRAM,VCF,BCF
Output data A file containing the best guess of the sample identity, with detailed statistics to reach to the best guess, a file containing the statistics for matching each cell with each possible sample, a file containing the statistics similar information to the previous one, but generated for sanity checking results and a file contains the statistics for matching each cell with each possible configuration of doublet.
Operating system Unix/Linux
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Requirements
htslib
Maintained Yes

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Maintainer


  • person_outline Hyun Min Kang <>

Publication for demuxlet

demuxlet institution(s)
Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA; Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA; Institute for Human Genetics (IHG), University of California, San Francisco, CA, USA; Institute for Computational Health Sciences, University of California, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA; Medical Scientist Training Program (MSTP), University of California, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, CA, USA; Diabetes Center, University of California, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Neurology, University of California, San Francisco, CA, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA; Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA; Department of Statistics, University of British Columbia, Vancouver, BC, Canada; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Lung Biology Center, University of California, San Francisco, CA, USA; Department of Orofacial Sciences, University of California, San Francisco, CA, USA
demuxlet funding source(s)
Supported by NIH R01AR071522 and R21AI133337; NIH F30DK115167, U01HL137182; NIH K25HL121295, R03DE025665; and Department of Defense W81WH-16-2-0018.

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