VCF-STATS(1)

💖 vcf-stats — like, the vibe check for your VCF file 💖

okay so bestie, this is vcf-stats, a User Command, and it's literally here to give you the statistic of VCF file. that's the whole name, that's the whole job. no cap. 🧬✨

✨ SYNOPSIS ✨

vcf-stats [OPTIONS] file.vcf.gz

that's it. that's the summoning circle. 🎀

💅 OPTIONS 💅

• -d, --dump <file> — take a dump file that already exists and recreate the files from it. lowkey a glow-up redo. (works with -p, iykyk 🫶)
• -f, --filters <filter1,filter2> — a whole list of filters, and each one looks like a column/field situation:
  • column/field (any value at all)
  • column/field=bin:max (clusters things into bins)
  • column/field=value (exact value only, periodt)
• -p, --prefix <dir/string> — the prefix for your output files. if there are slashes in there, directories will literally be created for you. ✨
• -s, --samples <list> — only process the samples you list here. use - for none. excluding samples you don't want may increase performance considerably, so like… why wouldn't you. 💀
• -h, -?, --help — this help message. hi bestie 👋

🌸 EXAMPLES 🌸

these are verbatim, don't @ me, just copy them exactly:

# Calculate stats separately for the filter field, quality and non-indels vcf-stats file.vcf.gz -f FILTER,QUAL=10:200,INFO/INDEL=False -p out/

# Calculate stats for all samples vcf-stats file.vcf.gz -f FORMAT/DP=10:200 -p out/

# Calculate stats only for the sample NA00001 vcf-stats file.vcf.gz -f SAMPLE/NA00001/DP=1:200 -p out/

vcf-stats file.vcf.gz > perl.dump

and that's the whole page, bestie 🦋 this was vcf-stats 0.1.5, dated July 2011 — yeah it's giving vintage but she still ate, and she's still the main character of your VCF stats. mwah 💖💅👑