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Structured data

Genome variation
a flexible framework for exploring genome variation
Programming Language

유전체 변이 분석 프로그램. SNV calling from NGS data의 결과 VCF와 혈연관계 정보 PED 파일을 입력하여 다양한 변이 분석을 수행한다. GEMINI는 GEnome MIMIng의 약어.

다음과 같은 기존 자료와의 비교 분석을 수행하고 분석 결과를 SQLite에 저장한다.

  1. ENCODE tracks
  2. UCSC Genome Browser tracks
  3. OMIM
  4. dbSNP
  5. KEGG
  6. HPRD

SNV 변이 분석은 다음 두가지 도구 가운데서 선택할 수 있다.

  1. VEP
  2. snpEff

빌트인 분석도구

  • comp_hets: Identifying potential compound heterozygotes
  • mendelian_error: Identify non-mendelian transmission.
  • de_novo: Identifying potential de novo mutations.
  • autosomal_recessive: Find variants meeting an autosomal recessive model.
  • autosomal_dominant: Find variants meeting an autosomal dominant model.
  • pathways: Map genes and variants to KEGG pathways.
  • interactions: Find genes among variants that are interacting partners.
  • lof_sieve: Filter LoF variants by transcript position and type
  • annotate: adding your own custom annotations
  • region: Extracting variants from specific regions or genes
  • windower: Conducting analyses on genome “windows”.
  • stats: Compute useful variant statistics.
  • burden: perform sample-wise gene-level burden calculations
  • ROH: Identifying runs of homozygosity
  • set_somatic: Flag somatic variants
  • actionable_mutations: Report actionable somatic mutations and drug-gene interactions
  • fusions: Report putative gene fusions
  • db_info: List the gemini database tables and columns

기본 사용법 #

VCF 데이터 정리 (split, left-align, trim variants)

$ vt decompose -s $VCF | vt normalize -r $REFERENCE - > $NEW_VCF

VCF 데이터 로드 (snpEff로 주석달기)

$ gemini load -v my.vcf -t snpEff my.db

기본 변이 검색 (Loss-of-function variant이면서 dbSNP에 없는 것)

$ gemini query -q "select * from variants where is_lof = 1 and in_dbsnp = 0" my.db

관련정보 #


관련 발표 - Exploring disease genetics from thousands of individual genomes with Gemini; SciPy 2013 Presentation

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