gigaBayes output format ... inconsistent with manual?

[jnfass]

I'm looking at my gigaBayes output, for which I've specified --o 3 so that I get individual allele counts, but not listings of each read. I'm getting a sub-field in the 9th column of the gff output that looks like this:

individualAlleleCounts=MID11:T|1|40|+|1|40|-|0|0&C|0|0|+|0|0|-|0|0,MID9:T|0|0|+|0|0|-|0|0&C|1|40|+|1|40|-|0|0

... but the manual only illustrates this field like so:

individualAlleleCounts=Person1:G|4|120&A|1|30,Person2:G|2|60&A|2|60

So, I understand that my results indicate, for individual "MID11", one read with a "T" base at this position, with base quality = 40. But what are the "+|1|40|-|0|0" fields ...? Sometimes they have positive values after the "+", and sometimes after the "-" ... and I don't see these "+" or "-" fields in the example output, nor can I find an explanation in the manual.

Does anyone know what these fields mean? I'm concerned that I'm missing something that gigaBayes is trying to tell me ...

~Joe

[Brad Chapman]

Joe;
I puzzled over that for a bit too. The individuals are separated by ','s and the bases within each individual by '&'s. For each base there are 3 components:

T|1|40| -- Base name, number of reads and quality
+|1|40| -- Number of reads and quality on positive strand
-|0|0 -- Number of reads and quality on negative strand

This lets you tease apart positive and negative strand contributions to a call. Hope this helps,
Brad

[jnfass]

ahhh! -- of course! Thanks Brad -- very helpful.
~Joe

[vinodyadav2083]

I have a quick question regarding GigaBayes GFF file format. I know it is now obsolete, and replaced by other tools. I couldn't find the manual either. But for a technical reason we desperately need to understand and use this format.

In the example below,in the column [AlleleA_Count], the first row has entry [ 1|0, 1/0|0/0 ]. Similarly,[ AlleleB_Count = 6|8, 2/4|1/7 ] What do these numbers mean in these two columns?

Chr SNV Start End SNV_Pvalue AlleleA AlleleA_Count AlleleB AlleleB_Count PR1701N///PR1701T_Genotype PR1701N///PR1701T_Genotype_Pvalue Status Allele Gene_Location Exon_Location SNV_Diff PR1701T

1 deletion 54723 54723 0.993229 T 1|0, 1/0|0/0 - 6|8, 2/4|1/7 T/-|-/- 0.986443|0.995399 Novel XX///XX Unkn NA 0 0

A quick reply will be greatly appreciated.
Many thanks in anticipation,