10 Variant Stratification

We currently output an intermediate VCF in GA4GH compatible format, meaning the results can be stratified and analyzed by hap.py's quantification helper script qfy.py. In order to use qfy.py please install hap.py. tabix and bgzip should already be included as part of HTSlib.

> ./vcfdist \                                 # run vcfdist
    query.vcf.gz \
    truth.vcf.gz \
    reference.fasta \
    -b analysis-regions.bed \
    -p output-prefix/
> bgzip output-prefix/summary.vcf             # compress summary VCF
> tabix -p vcf output-prefix/summary.vcf.gz   # index summary VCF
> export HGREF=/path/to/reference.fasta       # set reference path
> source /path/to/happy/venv2/bin/activate    # activate hap.py virtualenv
> python /path/to/happy/install/bin/qfy.py \  # run quantification script
    -t ga4gh \
    --write-vcf \
    --write-counts \
    --stratification strat.tsv \
    --roc QUAL \
    --o results/qfy-output-prefix \
    output-prefix/summary.vcf.gz

Ensure that strat.tsv contains one stratification region per line; each line consists of a region name and BED file name separated by a tab. GIAB stratification regions for GRCh38 can be found here.