
site_name: 'SnpEff & SnpSift Documentation'
site_description: 'SnpEff and SnpSift documentation'
site_author: 'Pablo Cingolani'
copyright: 'Pablo Cingolani'
repo_name: 'SnpEff'

repo_url: 'https://github.com/pcingola/SnpEff'
edit_uri: ''

docs_dir: 'src/docs'
site_dir: 'site'

extra_css:
  - 'stylesheets/extra.css'

theme:
  name: material
  palette:
      primary: 'indigo'
      accent: 'indigo'
  features:
      - tabs

markdown_extensions:
  - admonition
  - attr_list

extra:
  social:
    - icon: fontawesome/brands/linkedin
      link: 'http://www.linkedin.com/in/pablocingolani'
    - icon: fontawesome/brands/github-alt
      link: 'https://github.com/pcingola/SnpEff'

nav:
  - Home:
     - Home: index.md
     - Features: features.md
     - Usage examples: examples.md
     - Paper & Citations: citing.md
     - Who uses SnpEff?: users_of_snpeff.md
     - Integration: integration.md
     - License: license.md
     - Test cases: tests.md
  - SnpEff:
     - Introduction: se_introduction.md
     - Running SnpEff: se_running.md
     - Commands &amp; command line options: se_commandline.md
     - Input &amp; output files: se_inputoutput.md
     - Cancer samples: se_cansersamples.md
     - Additional annotations: se_additionalann.md
     - Output summary files: se_outputsummary.md
     - Troubleshooting: se_troubleshooting.md
     - Building databases: se_buildingdb.md
     - Building databases. Regulatory and Non-coding: se_buildingreg.md
     - Integration. GATK and Galaxy: se_integration.md
     - Commands and utilities: se_commands.md
     - Human Genomes: se_human_genomes.md
     - Frequently Asked Questions: se_faq.md
  - SnpSift:
     - Introduction: ss_introduction.md
     - SnpSift Filter: ss_filter.md
     - SnpSift Annotate: ss_annotate.md
     - SnpSift CaseControl: ss_casecontrol.md
     - SnpSift Intervals: ss_intervals.md
     - SnpSift Intervals Index: ss_intervalsindex.md
     - SnpSift Join: ss_join.md
     - SnpSift RmRefGen: ss_rmrefgen.md
     - SnpSift TsTv: ss_tstv.md
     - SnpSift Extract Fields: ss_extractfields.md
     - SnpSift Variant Type: ss_varianttype.md
     - SnpSift GWAS Catalog: ss_gwascatalog.md
     - SnpSift dbNSFP: ss_dbnsfp.md
     - SnpSift Split: ss_split.md
     - SnpSift PhastCons: ss_phastcons.md
     - SnpSift Concordance: ss_concordance.md
     - SnpSift Private: ss_private.md
     - SnpSift Vcf2Tped: ss_vcf2ped.md
     - SnpSift Intersect: ss_intersect.md
     - SnpSift RmInfo: ss_rminfo.md
     - SnpSift GeneSets: ss_genesets.md
     - SnpSift GT: ss_gt.md
     - SnpSift VcfCheck: ss_vcfcheck.md
     - Frequently asked questions: ss_faq.md
  - 'Download & Install':
     - Download and install: download.md
  - 'Examples':
     - Examples: examples.md
  - About:
     - About: about.md
     - Help and Bugs: help.md
     - In Memory: xiangyi_lu_donate.md
