input files GERMLINE

Question

[Alexandra]

Hi all! I'm having problems with the input files for running GERMLINE (ibd sharing).

I have a VCF file with phased data for chromosome 22. I converted it to ped/map files using ./impute_to_ped from GERMLINE package. Even though, the analisis was interrupted by a server error.

So, I'm thinking trying with GERMLINE2, but the input files requiered are haps file, sample filea and genetic map file. How do I get this files from de VCF file that I already have?

Please I need help with this, is the first time that I worked with this type of data.

[jv]

"Even though, the analisis was interrupted by a server error."

Are you saying that you got an error from GERMLINE when converting your VCF file to ped/map files? If so, posting you original command and the error is essential for allowing others to help you troubleshoot this issue. Or do you know for certain that GERMLINE is no longer a suitable option and that you must now use GERMLINE2?

[Alexandra]

At the end, the problem was the memory of my computer. But it worked with Germline2, which consume less memory. Thank you for replying.