$re = '/.*?chr(.*?)\.recalibrated.*/';
$str = 'output.chr10.recalibrated
output.chr11.recalibrated
output.chrY.recalibrated';
$subst = "\1";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php