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 <lparsons@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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