Brian Pardy (brianpardy)
Connected studies and activities

openSNP UbiQomix Microbiome Exploration Galileo Keeping Pace GenomiX Genome Exploration FamilyTreeDNA integration Gut Instinct Data sharing and ethical oversight Harvard Personal Genome Project Data Selfies Genome/Exome Upload American Gut Project 23andMe Upload Fitbit Connection Personal Data Notebooks Twitter Archive Analyzer Circles Cross-Genome Error Check Genevieve Genome Report The Preference Project Public Data Sharing
About me

My blog article on sharing my genome: https://pardydba.wordpress.com/2016/04/11/take-my-1000-genome-please/

My Genevieve report based upon my PGP-Veritas WGS: https://genevieve.herokuapp.com/genome_report/27/

My GenomiX project report: http://cs.wellesley.edu/~hcilab/pghci_compare/OpenHumans/report.php?m=17710924

mtDNA U2e1* (GenBank KU530226)

YDNA R-S1217/Z295* (YTree 26BS5)

Testing and analysis completed:

Whole genome sequence (first Veritas Genetics WGS customer)

mtDNA Sanger sequence (FTDNA)

YDNA STR-67 panel (FTDNA)

23andMe v3 chip

American Gut Project 5-site PGP participant sample

Circles in Human Biology photographic submission

Full Genomes Corp third party aDNA/mtDNA/YDNA WGS analysis

DNA.land SNP imputation from 23andMe v3 data

YFull analysis of Y-DNA from Veritas Genetics WGS - in progress

Public data

Data Selfies

26BS5.gtype.20131111.out
(3.3 MB) FGC - Y-SNP calling from Veritas Genetics WGS
26BS5.gtype.20151121supp.out
(1.0 MB) FGC - Y-SNP calling from Veritas Genetics WGS
26BS5.strcall203.lobystr203report.090913.ftdna.out
(1.3 KB) FGC - Y-STR calling of FTDNA markers from Veritas Genetics WGS
26BS5.strcall203.lobystr203report.090913.out
(169.5 KB) FGC - Y-STR calling of identified markers from Veritas Genetics WGS
26BS5.variantCompare.20140314.named.tab
(9.2 MB) FGC - Y-DNA variant calling from Veritas Genetics WGS
26BS5.vep_stats.html
(63.9 KB) FGC - variant effect predictor stats from Veritas Genetics WGS
26BS5.yknot.20151008.txt
(19.9 KB) FGC - yknot haplogroup calling from Veritas Genetics WGS
B2888-FASTA.fasta
(16.6 KB) FTDNA - Full mtDNA sequence U2e1*
WGC069899D.vcf.gz
(383.4 MB) Veritas Genetics WGS
haplogroup-r.org_WGC069899D_report.txt
(4.5 KB) haplogroup-r.org record for Veritas Genetics WGS with "private" Y-SNPs
snpEff_genes.tsv
(12.3 MB) FGC - snpEff by gene from Veritas Genetics WGS
snpEff_summary.html
(530.3 KB) FGC - SNP effect prediction summary from Veritas Genetics WGS

Genome/Exome Upload

hu9B93D0.vcf.gz
(383.4 MB) User-contributed VCF data
hu9B93D0.vcf.metadata.json
(470 bytes) VCF file metadata

American Gut Project

American-Gut-SAMEA4036965-ena-info.json
(2.3 KB) American Gut sample accession data from the European Nucleotide Archive, JSON format.
American-Gut-SAMEA4036965-ena-info.tsv
(1.8 KB) American Gut sample accession data from the European Nucleotide Archive, TSV format.
American-Gut-SAMEA4036965-metadata.json
(16.9 KB) American Gut sample survey data and metadata, JSON format.
American-Gut-SAMEA4036965-metadata.tsv
(13.0 KB) American Gut sample survey data and metadata, TSV format.
American-Gut-SAMEA4036965-run-ERR1459220.fastq.gz
(646.9 KB) American Gut 16S FASTQ raw sequencing data.
American-Gut-SAMEA4036966-ena-info.json
(2.3 KB) American Gut sample accession data from the European Nucleotide Archive, JSON format.
American-Gut-SAMEA4036966-ena-info.tsv
(1.8 KB) American Gut sample accession data from the European Nucleotide Archive, TSV format.
American-Gut-SAMEA4036966-metadata.json
(16.9 KB) American Gut sample survey data and metadata, JSON format.
American-Gut-SAMEA4036966-metadata.tsv
(13.0 KB) American Gut sample survey data and metadata, TSV format.
American-Gut-SAMEA4036966-run-ERR1459221.fastq.gz
(1.1 MB) American Gut 16S FASTQ raw sequencing data.
American-Gut-SAMEA4036967-ena-info.json
(2.3 KB) American Gut sample accession data from the European Nucleotide Archive, JSON format.
American-Gut-SAMEA4036967-ena-info.tsv
(1.8 KB) American Gut sample accession data from the European Nucleotide Archive, TSV format.
American-Gut-SAMEA4036967-metadata.json
(16.9 KB) American Gut sample survey data and metadata, JSON format.
American-Gut-SAMEA4036967-metadata.tsv
(13.0 KB) American Gut sample survey data and metadata, TSV format.
American-Gut-SAMEA4036967-run-ERR1459222.fastq.gz
(361.8 KB) American Gut 16S FASTQ raw sequencing data.
American-Gut-SAMEA4036968-ena-info.json
(2.3 KB) American Gut sample accession data from the European Nucleotide Archive, JSON format.
American-Gut-SAMEA4036968-ena-info.tsv
(1.8 KB) American Gut sample accession data from the European Nucleotide Archive, TSV format.
American-Gut-SAMEA4036968-metadata.json
(16.9 KB) American Gut sample survey data and metadata, JSON format.
American-Gut-SAMEA4036968-metadata.tsv
(13.0 KB) American Gut sample survey data and metadata, TSV format.
American-Gut-SAMEA4036968-run-ERR1459223.fastq.gz
(436.1 KB) American Gut 16S FASTQ raw sequencing data.
American-Gut-SAMEA4354028-ena-info.json
(2.3 KB) American Gut sample accession data from the European Nucleotide Archive, JSON format.
American-Gut-SAMEA4354028-ena-info.tsv
(1.8 KB) American Gut sample accession data from the European Nucleotide Archive, TSV format.
American-Gut-SAMEA4354028-metadata.json
(18.1 KB) American Gut sample survey data and metadata, JSON format.
American-Gut-SAMEA4354028-metadata.tsv
(14.0 KB) American Gut sample survey data and metadata, TSV format.
American-Gut-SAMEA4354028-run-ERR1546005.fastq.gz
(217 bytes) American Gut 16S FASTQ raw sequencing data.

Harvard Personal Genome Project

PGP-Harvard-hu9B93D0-surveys.json
(13.6 KB) PGP Harvard survey data, JSON format.

23andMe Upload

23andMe-genotyping.txt
(23.6 MB) 23andMe full genotyping data, original format
23andMe-genotyping.vcf.bz2
(8.9 MB) 23andMe full genotyping data, VCF format