How to read pysam SNPCaller output?

[aggp11]

Hello,

I am trying to identify the snps in my data and am using pysam's
SNPCaller for the same... I was wondering if someone can tell me what
the columns of the output represent.

for example one of the output line looks like:


0 9884 G S 108 108 59 509

The problem is that there is no header to the output.

I think, the second column is the position (0-based), third is the
reference base, last column is the number of reads.. However, I don't
understand what does S represent and the 108s.


I would really appreciate the help...


Thanks,


Praful Aggarwal

[ECO]

Moving to the correct forum.

[aggp11]

@ECO

I am sorry, but I didn't get you?