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
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
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