Hi,<div>We used the generate pileup tool with consensus base calling option using Maq. In the output, the quality scores of the bases were changed. For example if the input score of bases in the SAM file were &#39;IIJIH&#39;. They were changed to &#39;22321&#39;. Is this a glitch or is this expected? Thank you.
</div><div>Antony</div>