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Old 05-06-2019, 10:39 AM   #12
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Location: Seattle, WA

Join Date: Mar 2010
Posts: 5

The -o switch specifies the output file name, the -O switch specifies the format:

-O, --output-type <b|u|z|v> b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF

So -O z implies that the name should be basename.vcf.gz (or basename.vcf.bgz).

If you have a single variant you just want to examine, you could use -v and output to a standard vcf file (text).
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