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finished first round of JOSS draft
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‎.github/workflows/draft-pdf.yml‎

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name: Draft PDF
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on:
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push:
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paths:
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- paper/**
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- .github/workflows/draft-pdf.yml
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jobs:
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paper:
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runs-on: ubuntu-latest
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name: Paper Draft
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Build draft PDF
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uses: openjournals/openjournals-draft-action@master
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with:
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journal: joss
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# This should be the path to the paper within your repo.
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paper-path: paper/paper.md
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- name: Upload
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uses: actions/upload-artifact@v4
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with:
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name: paper
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# This is the output path where Pandoc will write the compiled
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# PDF. Note, this should be the same directory as the input
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# paper.md
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path: paper/paper.pdf

‎paper/paper.bib‎

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@misc{eigensoft_github,
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author = "Mah, Matthew and Patterson, Nick and Price, Alkes",
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title = {Eigensoft},
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year = {2021},
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publisher = {GitHub},
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journal = {GitHub repository},
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url = {https://github.com/DReichLab/EIG}
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}
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@ARTICLE{VCF,
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title = "The variant call format and {VCFtools}",
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author = "Danecek, Petr and Auton, Adam and Abecasis, Goncalo and Albers,
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Cornelis A and Banks, Eric and DePristo, Mark A and Handsaker,
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Robert E and Lunter, Gerton and Marth, Gabor T and Sherry,
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Stephen T and McVean, Gilean and Durbin, Richard and {1000
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Genomes Project Analysis Group}",
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journal = "Bioinformatics (Oxford, England)",
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publisher = "Oxford University Press (OUP)",
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volume = 27,
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number = 15,
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pages = "2156--2158",
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abstract = "Abstract Summary: The variant call format (VCF) is a generic
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format for storing DNA polymorphism data such as SNPs,
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insertions, deletions and structural variants, together with rich
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annotations. VCF is usually stored in a compressed manner and can
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be indexed for fast data retrieval of variants from a range of
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positions on the reference genome. The format was developed for
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the 1000 Genomes Project, and has also been adopted by other
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projects such as UK10K, dbSNP and the NHLBI Exome Project.
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VCFtools is a software suite that implements various utilities
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for processing VCF files, including validation, merging,
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comparing and also provides a general Perl API. Availability:
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http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk",
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month = "1~" # aug,
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year = 2011,
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url = "http://dx.doi.org/10.1093/bioinformatics/btr330",
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doi = "10.1093/bioinformatics/btr330",
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issn = "1367-4803,1367-4811",
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language = "en"
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}
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@ARTICLE{Price2006,
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title = "Principal components analysis corrects for stratification in
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genome-wide association studies",
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author = "Price, Alkes L and Patterson, Nick J and Plenge, Robert M and
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Weinblatt, Michael E and Shadick, Nancy A and Reich, David E",
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journal = "Nature genetics",
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publisher = "Nature Publishing Group",
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volume = 38,
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number = 8,
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pages = "904--909",
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month = "23~" # jul,
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year = 2006,
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url = "http://www.nature.com/doifinder/10.1038/ng1847",
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file = "All Papers/P/Price et al. 2006 - Principal components analysis corrects for stratification in genome-wide association studies.pdf",
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issn = "1061-4036"
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}
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@ARTICLE{1000_Genomes_Project_Consortium2015,
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title = "A global reference for human genetic variation",
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author = "{1000 Genomes Project Consortium} and {Corresponding authors} and
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{Steering committee} and {Production group} and {Baylor College
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of Medicine} and {Coriell Institute for Medical Research} and
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{Max Planck Institute for Molecular Genetics} and {US National
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Institutes of Health} and {Analysis group} and {Affymetrix} and
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{Albert Einstein College of Medicine} and {Harvard University}
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and {Human Gene Mutation Database} and {Icahn School of Medicine
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at Mount Sinai} and {Massachusetts General Hospital} and {McGill
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University} and {New York Genome Center} and {Ontario Institute
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for Cancer Research} and {Pennsylvania State University} and
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{Rutgers Cancer Institute of New Jersey} and {Tel-Aviv
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University} and {Jackson Laboratory for Genomic Medicine} and
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{Thermo Fisher Scientific} and University of California, San
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Francisco and {University of Chicago} and {University College
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London} and {University of Geneva} and {University of
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Montr\'{e}al} and {University of North Carolina at Chapel Hill}
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and {University of Puerto Rico} and {University of Texas Health
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Sciences Center at Houston} and {Structural variation group} and
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{BGI-Shenzhen} and {Bilkent University} and {Boston College} and
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{Cold Spring Harbor Laboratory} and {European Molecular Biology
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Laboratory} and {Leiden University Medical Center} and {Louisiana
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State University} and {McDonnell Genome Institute at Washington
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University} and University of California, San Diego and
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{University of Maryland School of Medicine} and {University of
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North Carolina at Charlotte} and {University of Oxford} and
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{University of Texas MD Anderson Cancer Center} and {University
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of Utah} and {University of Washington} and {Vanderbilt
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University School of Medicine} and {Weill Cornell Medical
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College} and {Wellcome Trust Sanger Institute} and {Exome group}
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and {Translational Genomics Research Institute} and {University
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of Michigan} and {Yale University} and {Functional interpretation
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group} and {Stanford University} and {Chromosome Y group} and
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{American Museum of Natural History} and {Arizona State
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University} and {Broad Institute of MIT and Harvard} and {Cornell
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University} and {European Molecular Biology Laboratory, European
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Bioinformatics Institute} and {University of Queensland} and
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{Virginia Bioinformatics Institute} and {Data coordination center
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group} and {Illumina} and University of California, Santa Cruz
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and {Samples and ELSI group} and {Sample collection} and
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Colombians in Medell\'{\i}n, Colombia Clm and {Finnish in Finland
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(FIN)} and {Iberian Populations in Spain (IBS)} and {Puerto
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Ricans in Puerto Rico (PUR)} and {African Caribbean in Barbados
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(ACB)} and {Esan in Nigeria (ESN)} and {Gambian in Western
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Division -- Mandinka (GWD)} and Kinh in Ho Chi Minh City, Vietnam
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(khv) and Punjabi in Lahore, Pakistan (pjl) and {Scientific
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management} and {Writing group} and {National Eye Institute, NIH}
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and {British from England and Scotland (GBR)} and {Han Chinese
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South (CHS)} and {Bengali in Bangladesh (BEB)} and Chinese Dai in
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Xishuangbanna, China (cdx) and {Indian Telugu in the UK (ITU) and
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Sri Lankan Tamil in the UK (STU)} and {Mende in Sierra Leone
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(MSL)} and Peruvian in Lima, Peru (pel)",
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journal = "Nature",
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publisher = "Nature Publishing Group",
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volume = 526,
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number = 7571,
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pages = "68--74",
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abstract = "The 1000 Genomes Project set out to provide a comprehensive
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description of common human genetic variation by applying
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whole-genome sequencing to a diverse set of individuals from
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multiple populations. Here we report completion of the project,
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having reconstructed the genomes of 2,504 individuals from 26
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populations using a combination of low-coverage whole-genome
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sequencing, deep exome sequencing, and dense microarray
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genotyping. We characterized a broad spectrum of genetic
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variation, in total over 88 million variants (84.7 million single
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nucleotide polymorphisms (SNPs), 3.6 million short
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insertions/deletions (indels), and 60,000 structural variants),
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all phased onto high-quality haplotypes. This resource includes
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>99\% of SNP variants with a frequency of >1\% for a variety of
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ancestries. We describe the distribution of genetic variation
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across the global sample, and discuss the implications for common
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disease studies.",
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month = "30~" # sep,
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year = 2015,
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url = "http://www.nature.com/doifinder/10.1038/nature15393",
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file = "All Papers/1/1000 Genomes Project Consortium et al. 2015 - 1000 Genomes Project Consortium et al... - Supplement.pdf;All Papers/1/1000 Genomes Project Consortium et al. 2015 - A global reference for human genetic variation.pdf",
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issn = "0028-0836"
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}
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@book{gatk,
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title={Genomics in the cloud: using Docker, GATK, and WDL in Terra},
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author={Van der Auwera, Geraldine A and O'Connor, Brian D},
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year={2020},
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publisher={O'Reilly Media}
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}
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@article{samtools,
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author = {Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng},
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title = "{Twelve years of SAMtools and BCFtools}",
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journal = {GigaScience},
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volume = {10},
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number = {2},
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year = {2021},
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month = {02},
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abstract = "{SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed \\>1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.}",
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issn = {2047-217X},
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doi = {10.1093/gigascience/giab008},
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url = {https://doi.org/10.1093/gigascience/giab008},
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note = {giab008},
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eprint = {https://academic.oup.com/gigascience/article-pdf/10/2/giab008/36332246/giab008.pdf},
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}
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@ARTICLE{Orlando2021,
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title = "Ancient {DNA} analysis",
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author = "Orlando, Ludovic and Allaby, Robin and Skoglund, Pontus and Der

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