VCF (Variant Call Format)

[Caesarius]

   The Tutorial page on this :

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load

I got these files from :

https://www.panzea.org/genotypes

   I am trying to :

     Data > 

                 Sort Genotype Files

     The only accepted file of the above selection is the 2nd in the picture :hmp321_agpv4_chr1.vcf

     

      but freezes above.

  My guess is that the 4th file should be the one Tassel be able to open ?

  Please help if you can !

Regards,

  Caesarius

[Caesarius]

I am working on a Windows.

[Caesarius]

[Peter Bradbury]

hmp321_agpv4_chr1.vcf.gz is a huge file. Even compressed it is over 4GB and that is just for chromosome 1. Unless you have a specific need for this dataset, you should try something smaller. Loading the whole thing into memory will take a while and use a lot of memory. If you want to work with the hmp321 data then if hmp321_agpv4_chr1.vcf.gx.tbi is present in the same directory, then TASSEL looks for that and loads it instead. The tbi file is an index file and loads quickly. Also, read https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf on reporting TASSEL issues. 

[Caesarius]

     Dr. Peter Bradbury,

Thank you for the insights. 

I am restated the issues in a possible more readable way:

Data > 

                 Sort Genotype Files

    here is the folder  with the files from panzea.org/genotypes

  

    However selecting the  *.tbi   or  *.md5 file results in :

selecting the *.gz file  :

   which never happens .

   This is how TBI file looks:

    I am not sure what concretely I have to do to move forward , since Tassel does not seem to look and load the TBI  file. 

    Regards,

  Caesarius

[Peter Bradbury]

Two points here.

1. I made a mistake about the index file. TASSEL uses .lix index files not .tbi. So, it does not recognize the .md5 or the .tbi files. When you attempt to load the gz file, TASSEL attempts to load the entire file into memory. If you wait long enough either the file will load or you will get an out of memory error, probably the latter unless you have more than 20 GB or more of RAM. I am not sure exactly how much memory is required.

2. When reporting problems with TASSEL, it really helps to follow the instructions in the file that I linked which describes how to report TASSEL issues and post the entire log file. That way we can tell what steps were followed and exactly where problems occur to help with trouble shooting.

Peter