SNPs coordination in *.gff file

[GoogleCodeExporter]

in the *.gff file i saw

h1isotig00815   gigaBayes       SNP     244     245     0.999792        .       
.       alleles=G,A;individualGenotypes= .....;

h1isotig00815   gigaBayes       SNP     248     249     0.999996        .       
.       alleles=A,T;individualGenotypes= ....;

h1isotig00815   gigaBayes       SNP     249     249     1       .       .       
alleles=G,T;individualGenotypes=....;

h1isotig00815   gigaBayes       SNP     249     250     1       .       .       
alleles=A,T;individualGenotypes=....;

h1isotig00815   gigaBayes       SNP     250     250     1       .       .       
alleles=A,G;individualGenotypes=.....;

to make it simple, i extracted snp information as following:
h1isotig00815    244     245     G      A
h1isotig00815    248     248     G      A
h1isotig00815    248     249     A      T
h1isotig00815    249     249     G      T
h1isotig00815    249     250     A      T
h1isotig00815    250     250     A      G
h1isotig00815    251     251     G      A

As you can see, the coordinations of different SNPs overlap with each other.
How to interpret this?

Thanks A Lot!

Regards,

Elzed 

Original issue reported on code.google.com by elzedliu on 30 Sep 2010 at 1:39

Attachments:

• mosaikAlignment_assembler_h1isotig00815.gff

[GoogleCodeExporter]

Hi Elzed,

We develop a new genetic-variant detector, FreeBayes, instead of gigaBayes, and 
no longer maintain gigaBayes.

We'll be glad if you can choose FreeBayes as your genetic-variant detector.

FreeBayes: http://bioinformatics.bc.edu/marthlab/FreeBayes

Original comment by WanPing....@gmail.com on 27 Oct 2010 at 4:09

• Changed state: Done

[GoogleCodeExporter]

Yes. Thanks for your recommendation. However, i got basically the same thing. 
The coordination of different SNPs overlap with each other.  This is quite 
wired. Would you please help me out?

Original comment by elzedliu on 28 Oct 2010 at 12:02

[GoogleCodeExporter]

Hi Elzed,

Do you mind to contact Erik who is the developer of FreeBayes, whose email 
address is erik.garrison@bc.edu?

Original comment by WanPing....@gmail.com on 28 Oct 2010 at 2:56