From b4d68c7bb88e67f2ce03db0c48dddd161dd56d2e Mon Sep 17 00:00:00 2001 From: Zafir Stojanovski Date: Wed, 16 Apr 2025 15:46:07 +0200 Subject: [PATCH] Update 04-VCF-files.md Render multi-sample table correctly --- docs/04-genomic-file-formats/04-VCF-files.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/docs/04-genomic-file-formats/04-VCF-files.md b/docs/04-genomic-file-formats/04-VCF-files.md index 07ddbb3..4e06848 100644 --- a/docs/04-genomic-file-formats/04-VCF-files.md +++ b/docs/04-genomic-file-formats/04-VCF-files.md @@ -23,12 +23,11 @@ These fields describe: As alluded to earlier, the VCF format is flexible in that it *may* specify one or more samples and indicate whether the sample contains any of the variants specified in the file. A simplified version of this would be something like: -**Chromosome** **Position** **ID** **REF** **ALT** **Sample1** **Sample2** **Sample3** +| Chromosome | Position | ID | REF | ALT | Sample1 | Sample2 | Sample3 | +|------------|------------|------------|-----|-----|---------|---------|---------| +| chr1 | 114713908 | rs11554290 | T | A | YES | NO | NO | +| chr17 | 7683718 | . | C | CT | NO | YES | YES | ---- - -chr1 114713908 rs11554290 T A YES NO NO -chr17 7683718 . C CT NO YES YES However, in practice this is complicated by the fact that variants can have various genotypes (homozygous reference allele, homozygous alternate allele, or heterozygous) and evidence depth. For more information, see the "Genotype fields" section of the [VCF specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf).