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Old 01-16-2020, 02:09 PM   #1
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Location: Poland

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Default Converting vcf.gz file into vcf


If there is any possibility to convert vcf.gz file into vcf file? I am not familiar with bioinformatic tools and I will be extremely grateful for any help.
Noveline is offline   Reply With Quote
Old 01-17-2020, 05:23 AM   #2
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The file extension indicates gzip compression. You should be able to use "gunzip" program to uncompress the file. On windows you may want to use a program such as 7-zip to do this conversion.
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Old 01-21-2020, 05:25 PM   #3
David Eccles (gringer)
Location: Wellington, New Zealand

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Have a look at the bcftools package. It supports uncompressed and gzip-compressed VCF file formats as input, as well as the BCF format, and provides means to output as any of those formats. Here are the first few lines of documentation for bcftools view:

$ bcftools view

About:   VCF/BCF conversion, view, subset and filter VCF/BCF files.
Usage:   bcftools view [options] <in.vcf.gz> [region1 [...]]

Output options:
    -G,   --drop-genotypes              drop individual genotype information (after subsetting if -s option set)
    -h/H, --header-only/--no-header     print the header only/suppress the header in VCF output
    -l,   --compression-level [0-9]     compression level: 0 uncompressed, 1 best speed, 9 best compression [-1]
    -o,   --output-file <file>          output file name [stdout]
    -O,   --output-type <b|u|z|v>       b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]
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