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Create reader for VCF (VCI) files #3

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jfoster17 opened this issue Jul 20, 2021 · 0 comments
Open

Create reader for VCF (VCI) files #3

jfoster17 opened this issue Jul 20, 2021 · 0 comments

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@jfoster17
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Note that we have both .vci.gz and .vci.tbi.gz files, the later of which probably supports fetching of only relevant portions fo the dataset.

Variant Call Format (VCF) is a flexible and extendable line-oriented text format developed by the 1000 Genomes Project for releases of single nucleotide variants, indels, copy number variants and structural variants discovered by the project. When a VCF file is compressed and indexed using tabix, and made web-accessible, the Genome Browser is able to fetch only the portions of the file necessary to display items in the viewed region.

http://genome-asia.ucsc.edu/goldenPath/help/vcf.html

The test files didn't immediately work for PyVCF (which seems to not be maintained

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