[Vcftools-announce] VCFtools v0.1.12

[Adam A. <ada...@gm...>]

Dear VCFtools users,

I'm pleased to announce the release of VCFtools v0.1.12, which was posted
as a tarball a few minutes ago.

This version can be downloaded from here:
http://sourceforge.net/projects/vcftools/files/

Version v0.1.12 represents a fairly major revision, and includes a number
of important changes and bug fixes. All users are encouraged to update as
soon as possible. Importantly, *this version includes support for working
on standard input and output streams*, which dramatically improves the
programs flexibility. For usage examples please visit this page:
http://vcftools.sourceforge.net/documentation.html

A list of changes follows this email.

Thank you,

Adam


Added options:
--stdout, -c : These options force the program to write to standard out
instead of directly to file
--relatedness2 : Calculate and output a relatedness statistic based on the
method of Manichaikul et al., Bioinformatics 2010

Removed options:
--min-indv-meanDP <float>
--max-indv-mean-DP <float>
--mind <float>
--recode-to-stream (functionality replaced by --recode used with --stdout)
--recode-bcf-to-stream (functionality replaced by --recode-bcf used with
--stdout)
--force-write-index

Changed options:
--vcf, --gzvcf, --bcf : These options now can accept a dash character "-"
instead of a filename, allowing the program to read from standard input.
--phased : Now this function only removes sites with unphased genotypes and
does not remove individuals with all unphased genotypes.
--missing : This function has been split into two separate functions that
provides the same functionality as the previously: --missing-indv and
--missing-site
--filtered-sites : This function has been split into two separate functions
that provides the same functionality as the previously: --kept-sites and
--removed-sites
--TsTv <int> : This function no longer outputs a summary along with the
TsTv bin file. To output only the summary file, use function: --TsTv-summary
--geno <float> : This option has been renamed --max-missing <float> but
keeps the same functionality.

-- 
Adam Auton
Assistant Professor,
Department of Genetics,
Albert Einstein College of Medicine,
1301 Morris Park Avenue,
Van Etten B06,
Bronx, New York 10461

Tel: +1 (718) 839 7216