Hi all, <br><br>I ran into this problem, and thought others might run in to it as well:<br>When using bowtie and samtools, positions are formatted with a 1-base offset, whereas interval format requires 0-base offset. <br>Recently, I used the &#39;Filter pileup on coverage and SNPs&#39; tool with the &#39;convert coordinates to intervals&#39; option, and used the output with the &#39;aaChanges&#39; tool to detect amino acid changes. <br>
In the aaChanges output there was an off-by-one discrepancy with a previous analysis, which brought this problem to my attention. <br>Should the &#39;Filter pileup&#39; 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.<br>
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.<br>
<br>Best,<br>Katie<br>