| Critical commercial assays |
|
| TruSeq DNA PCR-Free High Throughput Library Prep Kit |
Illumina |
Cat#20015963 |
| KAPA Library Quantification Kits - Complete kit (Universal) |
Roche |
Cat#07960140001 |
| HS NGS Fragment Kit |
Agilent |
Cat#DNF-474-0500 |
| Quant-iT PicoGreen dsDNA Assay Kit |
Life Technologies |
Cat#P7589 |
| IDT for Illumina – TruSeq DNA UD Indexes (Illumina, 20,022,370) |
Illumina |
Cat#20022370 |
| SPRIselect Beads |
Beckman Coulter |
Cat#B23318
|
| PhiX v3 Control |
Illumina |
Cat#FC-110-3001 |
| NovaSeq 6000 S4 Reagent Kit (300 cycles) |
Illumina |
Cat#20012866 |
| NovaSeq Xp Kit (4-lane) |
Illumina |
Cat#20021663 |
|
| Deposited data |
|
| raw sequence data FASTQ files |
This paper |
EMBL-EBI: PRJEB31736, EMBL-EBI: PRJEB36890 |
| CRAM alignment files |
This paper |
EMBL-EBI: PRJEB31736, EMBL-EBI: PRJEB36890 |
| CRAM alignment files |
This paper |
AnVIL: https://app.terra.bio/#workspaces/anvil-datastorage/1000G-high-coverage-2019/
|
| CRAM alignment files |
This paper |
NCBI: https://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/1000G_2504_high_coverage/
|
| CRAM alignment files |
This paper |
s3://1000genomes/1000G_2504_high_coverage/ |
| GVCFs |
This paper |
IGSR: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20190425_NYGC_GATK/raw_calls_updated/
|
| SNV/INDEL VCFs |
This paper |
EMBL-EBI: PRJEB55077 |
| SNV/INDEL VCFs |
This paper |
dbSNP: https://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?handle=1000G_HIGH_COVERAGE (dbSNP: 1000G_HIGH_COVERAGE) |
| SNV/INDEL VCFs |
This paper |
IGSR: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_raw_GT_with_annot/
|
| SNV/INDEL VCFs (2,504-sample subset generated for evaluation purposes) |
This paper |
EMBL-EBI: PRJEB55077 |
| SNV/INDEL VCFs (2,504-sample subset generated for evaluation purposes) |
This paper |
IGSR: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20190425_NYGC_GATK/
|
| Phased SNV/INDEL/SV VCFs |
This paper |
EMBL-EBI: PRJEB55077 |
| Phased SNV/INDEL/SV VCFs |
This paper |
IGSR: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/
|
| SV VCF |
This paper |
EMBL-EBI: PRJEB55077 |
| SV VCF |
This paper |
IGSR: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20210124.SV_Illumina_Integration/
|
| SV VCF |
This paper |
dbVar: nstd206 |
| lifted-over GRCh38 phase 3 1kGP SNV/INDEL VCFs |
This paper |
EMBL-EBI: PRJEB55077 |
| lifted-over GRCh38 phase 3 1kGP SNV/INDEL VCFs |
This paper |
IGSR: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/phase3_liftover_nygc_dir/
|
| Sample metadata file with pedigree and sex information |
This paper |
IGSR: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/1kGP.3202_samples.pedigree_info.txt
|
|
| Experimental models: Cell lines |
|
| genomic DNA from 3,202 samples from the 1000 Genomes Project |
Coriell Institute for Medical Research |
Data S1 |
|
| Software and algorithms |
|
| Absinthe |
github.com/nygenome/absinthe |
github.com/nygenome/absinthe |
| BCFtools v1.9, 1.12, and v1.15 |
Li (2011), Danecek et al. (2021)
|
http://samtools.github.io/bcftools/bcftools.html |
| BWA-MEM v0.7.15 |
Li (2013) |
http://bio-bwa.sourceforge.net/ |
| bedtools v2.26.0 |
Quinlan and Hall (2010) |
https://github.com/arq5x/bedtools2 |
| CrossMap v0.5.3 |
Zhao et al. (2014) |
https://github.com/liguowang/CrossMap |
| Eagle v2.4.1 |
Loh et al. (2016) |
https://alkesgroup.broadinstitute.org/Eagle/ |
| FastQC v0.11.3 |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| GATK v3.5 and v4.1 |
Van der Auwera and O'Connor (2020) |
https://gatk.broadinstitute.org/hc/en-us |
| GATK-SV |
Collins et al. (2020) |
https://github.com/talkowski-lab/svtk |
| hap.py v0.3.12 |
github.com/Illumina/hap.py |
github.com/Illumina/hap.py |
| IMPUTE v2.3.2 |
Howie et al. (2009) |
https://mathgen.stats.ox.ac.uk/impute/impute_v2.html |
| KING v2.2.3 |
Manichaikul et al. (2010) |
https://www.kingrelatedness.com/ |
| PanGenie v1.0.0 |
Ebler et al. (2022) |
https://github.com/eblerjana/pangenie |
| Paragraph v2.2b and v2.4a |
Chen et al. (2019) |
https://github.com/Illumina/paragraph |
| Picard v2.4.1 |
Van der Auwera and O'Connor (2020) |
https://broadinstitute.github.io/picard/index.html |
| Plink v1.90 and v2.0 |
Chang et al. (2015) |
https://www.cog-genomics.org/plink/1.9/ |
| QCTOOL v2.0.2 |
https://www.well.ox.ac.uk/∼gav/qctool_v2 |
https://www.well.ox.ac.uk/∼gav/qctool_v2 |
| R v3.6.1 |
https://www.r-project.org/ |
https://www.r-project.org/ |
| RTG Tools v3.8.2 |
Cleary et al. (2015) |
https://github.com/RealTimeGenomics/rtg-tools |
| Samtools v1.3.1 |
Li et al. (2009) |
http://www.htslib.org/ |
| SHAPEIT v2.r904 |
Delaneau et al. (2011) |
https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html |
| SHAPEIT4 v4.2.2 |
Delaneau et al. (2019) |
https://odelaneau.github.io/shapeit4/ |
| svtools |
Larson et al. (2019) |
https://github.com/hall-lab/svtools |
| Variant Effect Predictor (VEP) v104 |
McLaren et al. (2016) |
https://useast.ensembl.org/info/docs/tools/vep/index.html |
| VCFtools v0.1.12 |
Danecek et al. (2011) |
https://vcftools.github.io/index.html |
| VerifyBamID |
Jun et al. (2012) |
https://genome.sph.umich.edu/wiki/VerifyBamID |
| WhatsHap v0.18 |
Martin et al. (2016) |
https://whatshap.readthedocs.io/en/latest/ |
| LUMPY |
Layer et al. (2014) |
https://github.com/arq5x/lumpy-sv |
| Manta |
Chen et al. (2016) |
https://github.com/Illumina/manta |
| Wham |
Kronenberg et al. (2015) |
https://github.com/zeeev/wham |
| MELT |
Gardner et al. (2017) |
https://melt.igs.umaryland.edu/ |
| cn.MOPS |
Klambauer et al. (2012) |
https://bioconductor.org/packages/release/bioc/html/cn.mops.html |
| CNVNator |
Abyzov et al. (2011) |
https://github.com/abyzovlab/CNVnator |
| GATK-gCNV |
https://github.com/broadinstitute/gatk |
https://github.com/broadinstitute/gatk |
| VaPoR |
Zhao et al. (2017) |
https://github.com/mills-lab/vapor |
