EVA-3585 Cli documentation #45
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nitin-ebi
approved these changes
Jul 16, 2024
| ``` | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT [SampleIDs...] | ||
| ``` | ||
| Here's a small example to illustrate the structure of a VCF file: Example VCF file archived at EVA to be inserted |
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Example VCF file archived at EVA to be inserted is this a TODO ?
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@nitin-ebi yes still searching for a good example vcf file that we have archived at EVA
apriltuesday
approved these changes
Jul 17, 2024
| A VCF (Variant Call Format) file is a type of file used in bioinformatics to store information about genetic variants. It includes data about the differences (or variants) between a sample's DNA and a reference genome. Typically, generating a VCF file involves several steps: preparing your sample, sequencing the DNA, aligning it to a reference genome, identifying variants, and finally, formatting this information into a VCF file. The overall goal is to systematically capture and record genetic differences in a standardised format. A VCF file consists of two main parts: the header and the body. | ||
| Header: The header contains metadata about the file, such as the format version, reference genome information, and descriptions of the data fields. Each line in the header starts with a double ##, except for the last header line which starts with a single #. | ||
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| File format version |
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Guessing this is just a reminder for yourself? But somewhere in this section we could link to the VCF specification.
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great idea @apriltuesday
tcezard
approved these changes
Jul 29, 2024
Co-authored-by: April Shen <ashen@ebi.ac.uk> Co-authored-by: nitin-ebi <79518737+nitin-ebi@users.noreply.github.com>
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Eva-sub-cli documentation review