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Last update: 20241217

Metrics Bcftools stats

Usage Example:

# Run bcftools stats
echo "--Generating stats for file: ${vcf}"
bcftools stats "${vcf}" > "${stats_out}"

# Run plot-vcfstats
echo "--Generating plots for stats of file: ${vcf}"
plot-vcfstats -p "${plot_out}" "${stats_out}"

We use this in our study book for:

  1. bcftools stats and plot-vcfstats: 07c_qc_summary_stats.sh -> study_book/qc_summary_stats gVCF summary after HC