[Biopython-dev] Fwd: [VCFtools-spec] The BCF2 quick reference document is up on the 1000G wiki

Brad Chapman chapmanb at 50mail.com
Mon Jul 9 11:27:18 UTC 2012

Thanks for the heads up. I'm excited about BCF2 and am hopeful it'll
help with some of the painful parts of VCF, like subsetting large files
by samples. There is also a page about it on the Broad wiki with more details:


In terms of the representation, this stays close to VCF so shouldn't
change a lot of the API people see. The main changes would be on the
backend side where we'd like to be able to swap in and out BCF2 and VCF
(and GVF) transparently with no visible change to the programmer.


> This could be important for Lenna's GSoC project.
> Heng Li had developed the original binary VCF format,
> BCF, but IIRC he wasn't keen to push it as a standard -
> see also http://vcftools.sourceforge.net/specs.html and
> http://vcftools.sourceforge.net/bcf.pdf
> It looks like BCF2 could be more widely used...
> Peter
> ---------- Forwarded message ----------
> From: Eric Banks <ebanks at broadinstitute.org>
> Date: Thu, Jul 5, 2012 at 5:38 PM
> Subject: [VCFtools-spec] The BCF2 quick reference document is up on
> the 1000G wiki
> To: "1000ANALYSIS at LIST.NIH.GOV" <1000ANALYSIS at list.nih.gov>,
> "vcftools-spec at lists.sourceforge.net"
> <vcftools-spec at lists.sourceforge.net>
>   Hi everyone,
> At the last 1000G meeting we discussed BCF2, the official binary version
> of VCF.  The quick reference guide for BCF2 is now linked from the main
> VCF page on the 1000G wiki; you can access it directly here:
> http://www.1000genomes.org/sites/1000genomes.org/files/documents/bcfv2.pdf
> I take no credit for the document itself, which is really the work of
> Heng and Mark.  At this point, both the GATK and samtools can produce
> BCF files (and they will soon become our standard output format).  We
> encourage other producers of VCF to consider moving over to BCF2 too.
> Best,
> Eric
> --
> Eric Banks, PhD
> Broad Institute of Harvard and MIT
> ebanks at broadinstitute.org
> 617-714-7636
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