vcf(5)

🦋 vcf(5) 🦋 Bioinformatics formats

💖 NAME 💖

okay so the thing we're talking about is vcf, short for Variant Call Format. it's giving data file energy and I am obsessed 😭✨

🌸 DESCRIPTION 🌸

okay bestie, so the Variant Call Format (VCF) is a TAB-delimited format. every data line has the same fields in the same order, and it's giving spreadsheet but make it bioinformatics 💅

• 1, CHROM — the CHROMosome name 🧚
• 2, POS — the left-most POSition of the variant 📍
• 3, ID — a unique variant IDentifier 🪪
• 4, REF — the REFerence allele 📖
• 5, ALT — the ALTernate allele(s), comma-separated 🔀
• 6, QUAL — the variant/reference QUALity score 💯
• 7, FILTER — the FILTERs that got applied 🧹
• 8, INFO — INFOrmation about the variant, semicolon-separated 📋
• 9, FORMAT — the FORMAT of the genotype fields, colon-separated (this one's optional, no pressure) 🌈
• 10+, SAMPLE — SAMPLE genotypes and per-sample info (also optional) 🫶

okay now the INFO tags. these are the ones samtools and bcftools use, and I'm going to explain every single one because I care 🥹

• AF1 — max-likelihood estimate of the site allele frequency (AF) of the first ALT allele (double) ✨
• DP — raw read depth, without any quality filtering (int) 📊
• DP4 — # of high-quality reference forward bases, ref reverse, alternate for and alt rev bases (int[4]) 🧮
• FQ — consensus quality. positive means the sample genotypes are different, negative means they're not (int) ⚖️
• MQ — Root-Mean-Square mapping quality of the covering reads (int) 🗺️
• PC2 — Phred probability of AF in group1 samples being larger (,smaller) than in group2 (int[2]) 🎲
• PCHI2 — posterior weighted chi^2 P-value between group1 and group2 samples (double) 🧪
• PV4 — P-value for strand bias, baseQ bias, mapQ bias and tail distance bias (double[4]) 🔍
• QCHI2 — Phred-scaled PCHI2 (int) 🌡️
• RP — # of permutations yielding a smaller PCHI2 (int) 🔁
• CLR — Phred log ratio of genotype likelihoods with and without the trio/pair constraint (int) 👨‍👩‍👧
• UGT — most probable genotype configuration without the trio constraint (string) 🧬
• CGT — most probable configuration with the trio constraint (string) 🧬✨
• VDB — tests variant positions within reads. it's meant for filtering RNA-seq artifacts around splice sites (float) ✂️
• RPB — Mann-Whitney rank-sum test for tail distance bias (float) 🏁
• HWE — Hardy-Weinberg equilibrium test (Wigginton et al) (float) ⚗️

🦄 SEE ALSO 🦄

• https://github.com/samtools/hts-specs — the full VCF/BCF file format spec, the ultimate source of truth 📚
• A note on exact tests of Hardy-Weinberg equilibrium — Wigginton JE et al PMID:15789306 📝

bestie that's the whole tea 🫶💜 this page is from htslib, dated August 2013, and it's vcf(5) forever 🧚✨