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duncanca / mosaik-aligner

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Unclear Gigabayes 0utput #43

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
I ran gigabayes with --anchor. I find it difficult to interpret the output.

For Eg, 

contig00396     gigaBayes       SNP     282     283     1       .       . 
     alleles=T,A;individualGenotypes=30PCUS:TA|1,contig00396:TA|0.5

The program calls it a SNP, and starts at 282 and ends at 283. Is this a
SNP or an Indel?  

The reference base at position 282 is T (281 is G, 283 is C), the program
shows  contig00396:TA. What does this mean? I expect the program to show
the reference base and also the variant base in the output when I use the
--anchor option.

Tina.

Original issue reported on code.google.com by tina.gra...@gmail.com on 5 Mar 2010 at 10:20

GoogleCodeExporter commented 8 years ago 
Hi Tina,

We no longer maintain gigaBayes, but we have a new genetic-variant detector, 
FreeBayes. Also, the developer, Erik, is very good at helping people, and 
incredibly thorough.

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

Original comment by WanPing....@gmail.com on 27 Oct 2010 at 4:20