SNV Frequencies Australia MGRB 4k WGS Track Settings
Version: Phase 3 Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
The Australian
Medical Genome Reference Bank (MGRB) collected whole-genome sequencing data of 4,011 healthy
elderly individuals who lived ≥70 years, so the dataset is depleted of damaging genetic
variants. Age and sex summary graphs are available from
the MGRB website.
Data Access
Due to license restrictions, the data for this track cannot be downloaded from the UCSC
Genome Browser. The Table Browser, Data Integrator, and download server are not available
for this track.
VCF access can be requested via a form from
Sydney Genomics.
Methods
The 4,011 MGRB samples underwent whole-genome sequencing on Illumina HiSeq X instruments at KCCG
under ISO 15189 accreditation, with paired-end TruSeq DNA Nano libraries sequenced one lane per
sample. Sequence reads were aligned to the hg38 reference genome assembly with bwa 0.7.15-r1140.
Variants were called with GATK 4.1.4.0 following the Genome Analysis Toolkit (GATK) best practices
procedure. A sites-only VCF with only passing variants (FILTER=PASS) was made with bcftools 1.20.
We received VCF files from m.hobbs@garvan.org.au via a transfer link and imported them.
The makeDoc file of the track documents how all source files of the varFreqs track were converted.
For some tracks, python scripts were needed; these are available from GitHub.