dzyim / human-genetic-variation

Human genome resequencing and variant calling

Human Genome Resequencing and Variant Calling

Software

Preprocessing

• [Adapter trimming]
• [Quality control]

Alignment

• BWA (http://bio-bwa.sourceforge.net/)
• Picard (https://broadinstitute.github.io/picard/)
• Samtools (http://www.htslib.org/)

Small Variant Calling

• GATK (https://gatk.broadinstitute.org/)
• Samtools (http://www.htslib.org/)
• BCFtools (http://www.htslib.org/)

Copy Number Variant Calling

Structural Variant Calling

Projects

International HapMap Project

• Overview (with a list of papers): https://www.genome.gov/10001688/international-hapmap-project
• Data: https://ftp.ncbi.nlm.nih.gov/hapmap/

1000 Genomes Project

• Overview (with publications): https://www.internationalgenome.org/1000-genomes-summary
• Data: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
• Data file formats: https://www.internationalgenome.org/formats
• View data for a specific variation and search by rsID in Ensembl

NHLBI Grand Opportunity Exome Sequencing Project (ESP)

• Exome Variant Server (with data downloads): https://evs.gs.washington.edu/EVS/
• FTP: http://ftp.ebi.ac.uk/pub/databases/eva/PRJEB5439/
• Article: https://doi.org/10.1126/science.1219240
• SNP calling pipeline: https://genome.sph.umich.edu/wiki/UMAKE or https://github.com/statgen/gotcloud

Exome Aggregation Consortium (ExAC)

• Home (no longer available): https://exac.broadinstitute.org/
• Data: https://gnomad.broadinstitute.org/downloads#exac-variants
• Article: https://www.nature.com/articles/nature19057

Genome Aggregation Database (gnomAD)

• Home: https://gnomad.broadinstitute.org/
• Data: https://gnomad.broadinstitute.org/downloads
• Article: https://www.nature.com/articles/s41586-020-2308-7

NHLBI Trans-Omics for Precision Medicine (TOPMed)

• Home: https://topmed.nhlbi.nih.gov/
• BRAVO (BRowse All Variants Online) variant browser: https://bravo.sph.umich.edu/
• TOPMed Imputation Server: https://imputation.biodatacatalyst.nhlbi.nih.gov/#!
• Article: https://www.nature.com/articles/s41586-021-03205-y

UK10K project

• Home: https://www.uk10k.org/
• Data links: https://www.uk10k.org/data.html
• Publications: https://www.uk10k.org/publications.html

100,000 Genomes Project

• Home: https://www.genomicsengland.co.uk/initiatives/100000-genomes-project
• Public Involvement in Global Genomics Research: https://doi.org/10.3389/fpubh.2019.00079
• Publications that include the Genomics England dataset: https://www.genomicsengland.co.uk/research/publications

UK Biobank

• Home: https://www.ukbiobank.ac.uk/
• About the data: https://www.ukbiobank.ac.uk/enable-your-research/about-our-data
• Publications: https://www.ukbiobank.ac.uk/enable-your-research/publications
• Exome sequencing paper: https://www.nature.com/articles/s41586-021-04103-z
• Whole genome sequencing paper: https://www.nature.com/articles/s41586-022-04965-x