Output VCF.gz is not block compressed

williamslab / ped-sim

Pedigree simulator

GNU General Public License v3.0

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Output VCF.gz is not block compressed #7

Closed nh13 closed 5 years ago

nh13 commented 5 years ago

When the input VCF is compressed (.gz using bgzip), the output should also be block-compressed. Unfortunately, it is gzip compressed. This is not compatible with downstream tools. See how samtools/htslib outputs vcfs.

williamslab commented 5 years ago

Yes, this is an issue. I don't have the bandwidth to look up how to use the bgzip libraries currently. I'm open to you submitting a pull request if you code support for bgzip format output.