Il 2014-06-30 18:40 Anton Nekrutenko ha scritto:
Lance:

Here is github URL:

https://github.com/nekrut/freebayes [3]

 On Wed, Jun 25, 2014 at 2:40 PM, Lance Parsons
<lpars...@princeton.edu [4]> wrote:

Thanks for the major update of the Freebayes wrapper, excellent!

I've run into two issues, however.

1) When using "set allelic scope" I get the following error:

Fatal error: Exit code 1 ()
freebayes: unrecognized option `--min-repeat-length'
did you mean --min-repeat-size ?

This bug (and other 2) would be fixed by this pull request:

https://github.com/nekrut/freebayes/pull/1

Best,
Nicola

2) When using a vcf file as input I get the following error:

Fatal error: Exit code 1 ()
open: No such file or directory
[bgzf_check_bgzf] failed to open the file: input_variant_vcf.vcf.gz
[tabix++] was bgzip used to compress this file?
input_variant_vcf.vcf.gz

I'd be happy to help resolve these.  Is there a bitbucket repo
somewhere to submit pull requests?

--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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--

Anton Nekrutenko
Associate Professor
Dept. of Biochemistry and Molecular Biology
http://nekrut.bx.psu.edu [5]
 (814) 826-3051

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