"Filter pileup" outputs 0-based coordinates if you use the "Convert
coordinates to intervals" option. So the issue may be related to aaChanges
tools. Can you give us a specific example, so we can track things down.
On May 12, 2011, at 10:37 AM, Katie Hyma wrote:
> Hi all,
> I ran into this problem, and thought others might run in to it as well:
> When using bowtie and samtools, positions are formatted with a 1-base offset,
> whereas interval format requires 0-base offset.
> Recently, I used the 'Filter pileup on coverage and SNPs' tool with the
> 'convert coordinates to intervals' option, and used the output with the
> 'aaChanges' tool to detect amino acid changes.
> In the aaChanges output there was an off-by-one discrepancy with a previous
> analysis, which brought this problem to my attention.
> Should the 'Filter pileup' tool be changed to produce output with 0-base
> offset when interval format is selected, since interval format is defined as
> having 0-base output? It seems that others might run into the same problem,
> and it would be an easy one to miss.
> Although the pileup format is now deprecated, the same problem might occur
> if/when the change to VCF format occurs, as it also uses 1-base offset. It
> also may be a problem for other tools that use interval format as an input,
> expecting a 0-based position.
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