| Deposited data |
|
| Raw (FASTQ) and reference mapped (BAM) reads |
This study |
ENA: PRJEB71943
|
| Supplemental Figures, Tables, and Files |
This study |
Mendeley Data: https://doi.org/10.17632/ts4vc55rzp.1
|
| Human reference genome NCBI build 37, GRCh37, decoy version |
The 1000 Genomes Project Consortium et al.100
|
https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz |
| Raw (FASTQ) or (BAM/CRAM) reads |
The 1000 Genomes Project Consortium et al.100
|
https://www.ebi.ac.uk/ena/browser/view/PRJEB31736 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Bergström et al.13
|
https://www.ebi.ac.uk/ena/browser/view/PRJEB6463 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Kars et al.101
|
https://www.ebi.ac.uk/ena/browser/view/PRJNA674530 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Mallick et al.11
|
https://www.ebi.ac.uk/ena/browser/view/PRJEB9586 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Wong et al.102
|
https://www.ncbi.nlm.nih.gov/biosample/?term=SS6003405; https://www.ncbi.nlm.nih.gov/biosample/?term=SS6003411; https://www.ncbi.nlm.nih.gov/biosample/?term=SS6003413; https://www.ncbi.nlm.nih.gov/biosample/?term=SS6003435
|
| Raw (FASTQ) or (BAM/CRAM) reads |
Yang et al.103
|
https://ngdc.cncb.ac.cn/gsa/search?searchTerm=PRJCA000457 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Karmin et al.3
|
https://www.ebi.ac.uk/ena/browser/view/PRJEB8108 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Rodriguez-Flores et al.104
|
https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR2098261&display=download |
| Raw (FASTQ) or (BAM/CRAM) reads |
Carmi et al.105
|
https://ega-archive.org/search/egad00001000781 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Haber et al.106; Gilly et al.107
|
https://ega-archive.org/datasets/EGAD00001001440 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Serra-Vidal et al.108
|
https://www.ebi.ac.uk/ena/browser/view/PRJEB29142 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Alsmadi et al.109
|
https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR1274979&display=download |
| Raw (FASTQ) or (BAM/CRAM) reads |
Ilyas et al.110
|
https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR926184&display=download |
| Raw (FASTQ) or (BAM/CRAM) reads |
Kaja et al.92
|
The Thousand Polish Genomes: 633_28990_20 |
| Raw (FASTQ) or (BAM/CRAM) reads |
Almarri et al.68
|
https://www.ebi.ac.uk/ena/browser/view/PRJEB28504 |
|
| Software and algorithms |
|
| SAMtools v1.9 |
Li et al.111
|
http://www.htslib.org |
| BEDtools v2.24 |
Quinlan and Hall112
|
https://bedtools.readthedocs.io/en/latest |
| BWA-MEM v0.7.17 |
Li and Durbin113; Li114
|
http://bio-bwa.sourceforge.net |
| Picard-tools-2.0.1 |
N/A |
http://broadinstitute.github.io/picard |
| GATK-3.5 |
McKenna et al.115
|
https://gatk.broadinstitute.org/hc/en-us |
| BCFtools v1.6 |
Danecek et al.116
|
https://www.htslib.org |
| R v4.3.3 |
R CoreTeam66
|
https://cran.r-project.org/bin/windows/base/ |
| RStudio Build 402 |
RStudio Team67
|
|
| BEAST v1.10.4 |
Suchard et al.80
|
https://beast.community |
| spreaD3 v0.9.7.1rc |
Bielejec et al.81
|
https://rega.kuleuven.be/cev/ecv/software/SpreaD3 |
| RAxML v7.3.2 |
Stamatakis117
|
https://github.com/stamatak/standard-RAxML |
| BEAGLE library v3.1.2 |
Ayres et al.118
|
https://beast.community/beagle |
| Tracer v1.7 |
Rambaut et al.119
|
https://beast.community/tracer |
| LogCombiner v1.10.4 |
Drummond and Rambaut120
|
https://beast.community/logcombiner |
| TreeAnnotator v1.10.4 |
Drummond and Rambaut120
|
https://beast.community/treeannotator |
| Surfer v8 |
Relethford121
|
https://www.goldensoftware.com/products/surfer/ |
| pathPhynder |
Martiniano et al.122
|
https://github.com/ruidlpm/pathPhynder |
| Python v3.8.0 |
Van Rossum and Drake123
|
https://www.python.org |
| FigTree v1.4.4 |
N/A |
http://tree.bio.ed.ac.uk/software/figtree/ |
