| Biological Samples |
|
| HGDP-CEPH Human Genome Diversity Cell Line Panel |
CEPH (Centre d’Etude du Polymorphism) |
http://www.cephb.fr/en/hgdp_panel.php |
| Melanesian lymphoblastoid cell lines |
Coriell Institute for Medical Research |
GM10543 and GM10540 |
|
| Critical Commercial Assays |
|
| Phase-Prep BAC DNA kit |
Sigma-Aldrich |
NA0100 |
| the GenomePlex Complete Whole Genome Amplification kit |
Sigma-Aldrich |
WGA2 |
| GenomePlex Complete Whole Genome Reamplification kit |
Sigma-Aldrich |
WGA3 |
|
| Deposited Data |
|
| 1000 Genomes Project Structural Variation Callset |
Sudmant et al., 2015a |
https://www.internationalgenome.org/phase-3-structural-variant-dataset |
| SGDP Structural Variation Callset |
Sudmant et al., 2015b |
Supplementary table from study |
| HGDP SNV Callset |
Bergström et al., 2020 |
ftp://ngs.sanger.ac.uk/production/hgdp |
| HGDP Structural Variation Callset |
This study |
ftp://ngs.sanger.ac.uk/scratch/project/team19/HGDP_SV/ |
|
| Software and Algorithms |
|
| GenomeSTRiP v2.00 |
Handsaker et al., 2015 |
http://software.broadinstitute.org/software/genomestrip/ |
| Manta v1.6 |
Chen et al., 2016 |
https://github.com/Illumina/manta |
| GraphTyper v2.0 |
Eggertsson et al., 2019 |
https://github.com/DecodeGenetics/graphtyper |
| svimmer |
N/A |
https://github.com/DecodeGenetics/svimmer |
| LiftOver |
UCSC Genome Browser |
https://genome.ucsc.edu/cgi-bin/hgLiftOver |
| plink2 |
Chang et al., 2015 |
https://www.cog-genomics.org/plink/2.0/ |
| R-3.6.0 |
https://www.r-project.org/ |
https://www.r-project.org/ |
| EIGENSTRAT |
Price et al., 2006 |
https://github.com/DReichLab/EIG/tree/master/EIGENSTRAT |
| Vcflib |
N/A |
https://github.com/vcflib/vcflib |
| bwa v0.7.12 |
Li & Durbin 2009 |
https://github.com/lh3/bwa |
| Picard v2.6.0 |
N/A |
http://broadinstitute.github.io/picard/ |
| IGV |
Thorvaldsdóttir et al., 2013 |
http://software.broadinstitute.org/software/igv/ |
| Long Ranger v2.12 |
Marks et al., 2019 |
https://support.10xgenomics.com/genome-exome/software/downloads/latest |
| Supernova v2.1.1 |
Weisenfeld et al., 2017 |
https://support.10xgenomics.com/de-novo-assembly/software/downloads/latest |
| NUI pipeline |
Wong et al., 2018 |
https://github.com/wongkarenhy/NUI_pipeline |
| Variant Effect Predictor |
McLaren et al., 2016 |
http://asia.ensembl.org//useast.ensembl.org/info/docs/tools/vep/index.html?redirectsrc=//asia.ensembl.org%2Finfo%2Fdocs%2Ftools%2Fvep%2Findex.html |
| Bcftools |
N/A |
http://samtools.github.io/bcftools/ |
| Loupe Genome Browser |
N/A |
https://support.10xgenomics.com/genome-exome/software/downloads/latest |
