Var-md : How do use it ?

[jpofmars]

Hello,

Somebody knows Var-md (VAR-MD: A tool to analyze whole exome/genome variants in small human pedigrees with Mendelian inheritance.) ?

I want to test it, but I don't find the documentation.

For exemples, it seems that the tool needs a configuration file but I don't know how to generate it.


research.nhgri.nih.gov/software/Var-MD/


thanks,

jp

[msincan]

Configuration file

The configuration file is important but not enough, it simply has paths to all the input and annotation data files and a few parameters. I'll update the web site with some documentation shortly (i.e next week)
One needs to create some intermediary files (e.g a local dbsnp sqlite database etc) to take full advantage of all the functions. Please send me an e-mail if you have immediate specific questions until the web site is updated.
Thanks

[jpofmars]

cool !
I wait the update and the doc to test that.

Thanks

[ElGamal]

Hello,

I'm also interested in this tool. Is there already an updated version with documentation and the config file online?
That would be great.

Thanks

[msincan]

Please see http://code.google.com/p/var-md/ for additional information. Please let me know if you need more info and I'll update the wiki.
Thanks

[ElGamal]

Yeah, thats great. Thank you very much - I think this should be sufficient.
Andy

Edit:
Is there a possibiblity to convert those input NISC and NextGene generated variant reports to the VCF (Variant Call Format) version 4.0 format (http://www.1000genomes.org/node/101)?
I only have those VCF-files and would be glad if this tool would support those in any way

[ElGamal]

I created a script to convert a vcf fiel to this VS format and it should work.
But when I want to start the python script only 14 files (11 of them ar sh-files) were created in the specific tmp folder but tehre are no result files.

The start command is: python varmd.py --config study.cfg --func run_analysis

and the config file contains:
input_file, input_include_bed_file, input_bam_file1, input_bam_file2, interval 20000000, nodetype norm, population_file, liftOver_path and liftOver_chain_path

What have I done wrong?
Wich file are necessary to be able to start the tool?

I hope you can help me.
Regards,
Andy