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Genomic Reference Data

This directory contains curated datasets for benchmarking variant calls. Large files (VCFs, BED) are gitignored and must be downloaded separately.

Platinum Genomes Truth Set VCFs

High-confidence variant calls for NA12877 and NA12878 (hg38/GRCh38).

Download from AWS S3:

aws s3 cp --no-sign-request \
  s3://platinum-genomes/2017-1.0/hg38/small_variants/NA12877/ \
  data/PlatinumGenomesIllumina/vcf/ --recursive

Download from Illumina FTP:

wget -P data/PlatinumGenomesIllumina/vcf/ \
  ftp://platgene_ro@ussd-ftp.illumina.com/2017-1.0/hg38/small_variants/NA12877/NA12877.vcf.gz \
  ftp://platgene_ro@ussd-ftp.illumina.com/2017-1.0/hg38/small_variants/NA12877/NA12877.vcf.gz.tbi \
  ftp://platgene_ro@ussd-ftp.illumina.com/2017-1.0/hg38/small_variants/NA12878/NA12878.vcf.gz \
  ftp://platgene_ro@ussd-ftp.illumina.com/2017-1.0/hg38/small_variants/NA12878/NA12878.vcf.gz.tbi

See PlatinumGenomesIllumina/README.md for full details.

Confident Regions BED

High-confidence genomic intervals for restricting benchmarking comparisons (Platinum Genomes 2017-1.0, hg38).

Download from AWS S3:

aws s3 cp --no-sign-request \
  s3://platinum-genomes/2017-1.0/hg38/small_variants/ConfidentRegions.bed.gz \
  data/ConfidentRegions/
gunzip data/ConfidentRegions/ConfidentRegions.bed.gz

See ConfidentRegions/README.md for full details.

Reference Genome

You also need an hg38 reference FASTA with .fai and .dict index files. This is not included in this repository. Common sources: