Yes. I haven't found it documented anywhere, but I ran a simple test:
$ bcftools view -Oz --no-version foo.vcf > bar.vcf.gz
$ md5sum bar.vcf.gz
18a2f494710cf170ba79892936015ba8 bar.vcf.gz
$ gunzip bar.vcf.gz
$ bgzip bar.vcf
$ md5sum bar.vcf.gz
18a2f494710cf170ba79892936015ba8 bar.vcf.gz
$ gunzip bar.vcf.gz
$ gzip bar.vcf
$ md5sum bar.vcf.gz
9f5b1cf654966912b78a9cb7175ffc2c bar.vcf.gz
I passed a vcf file through bcftools view -Oz
, checked the md5sum
of the resulting file, then uncompressed it and recompressed with bgzip
and confirmed that the resulting file had the same md5sum
. Finally, I also compressed using normal gzip
to be sure that the md5sum
would be different, as it was.
So yes, it does indeed look like bcftools
creates files that are the same as though you'd passed them through bgzip
.