A little while ago I wrote some code for annotating images that works equally well for annotating PDF files inside beamer. My macros define an AnnotatedImage environment where the coordinates are scaled so that the rectangular image fits inside a suitably scaled unit square, which makes it pretty easy to draw on the image. For example, you can produce the following "beamer slide"

using the essentially the code:
\begin{AnnotatedImage}[width=0.8]{abacus.pdf}
\draw[red, rounded corners, thick](0.2,0.85) rectangle(0.5,0.71);
\draw[<-,red](0.2,0.78)--++(-0.1,0);
\end{AnnotatedImage};
[This MWE will not compile as I used a random PDF file abacus.pdf on my computer and you won't have this...unfortunately, nice packages like mwe don't supply PDF files.] The optional argument to the environment allows you set the mage dimensions and inside the environment you can use arbitrary tikz commands. In addition, there is also a \annotate command. See Image with some overlaid text for more details.
For a multi-page PDF file this almost certainly won't work but it will work if you extract the pages that you want to annotate. The other option would be to be use pdfpages to extract only the pages that you need. If you need this let me know as it shouldn't be hard to modify my code to use pdfpages directly.
Here is the full code:
\documentclass{beamer}
\usepackage{tikz}
\usepackage{xparse}
\tikzset{% styling for the overlay
annotatedImage/x/.initial = 0.7,% default overlay position
annotatedImage/y/.initial = 0.7,
annotatedImage/width/.initial = 1,% default image width
annotatedImage/.unknown/.code = {% unknown keys are appended to style
% to append to a style we need to expand everything first
\edef\tikzappend{\noexpand\tikzset{annotatedImage/.append style =
{\pgfkeyscurrentname=\pgfkeyscurrentvalue}}}
\tikzappend
},
annotatedImage/.style = {% default overlay style
draw=red, ultra thick, rounded corners, rectangle,
}
}
\newsavebox\annotatedImageBox% need to calculate the width and height
% internal helper functions
\newcommand\AnnotatedImageVal[1]{\pgfkeysvalueof{/tikz/annotatedImage/#1}}
\newcommand\SetUpAnnotatedImage[2]{% set keys and dimensions to scale image
\tikzset{annotatedImage/.cd, #1}%
\sbox\annotatedImageBox{\includegraphics[width=\AnnotatedImageVal{width}\textwidth,
keepaspectratio]{#2}}%
\pgfmathsetmacro\annotatedHeight{\ht\annotatedImageBox/28.453}% convert from px to a tikz length
\pgfmathsetmacro\annotatedWidth{\wd\annotatedImageBox/28.453}%
}
% usage: \annotatedImage[node options]{image}{text}
\NewDocumentCommand\annotatedImage{ O{} m m}{%
\bgroup% start a group to keep tikz changes local
\SetUpAnnotatedImage{#1}{#2}%
\begin{tikzpicture}[xscale=\annotatedWidth, yscale=\annotatedHeight]%
\node[inner sep=0, anchor=south west] (image) at (0,0) {\usebox{\annotatedImageBox}};
\node[annotatedImage] at (\AnnotatedImageVal{x},\AnnotatedImageVal{y}) {#3};
\end{tikzpicture}%y
\egroup%
}
% usage: \annotate <insert favourite node commands>;
\newcommand\annotate[1][]{\node[annotatedImage,#1]}
% usage: \begin{AnnotatedImage][width(default 1)]{image} tikz commands....\end{AnnotatedImage}
\newenvironment{AnnotatedImage}[2][1]{%
\SetUpAnnotatedImage{#1}{#2}%
\tikzpicture[xscale=\annotatedWidth, yscale=\annotatedHeight]
\node[inner sep=0, anchor=south west] at (0,0) {\usebox{\annotatedImageBox}};
}{\endtikzpicture}
\begin{document}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}{PDF example}
\begin{AnnotatedImage}[width=0.8]{abacus.pdf}
\draw[red, rounded corners, thick](0.2,0.85) rectangle(0.5,0.71);
\draw[<-,red](0.2,0.78)--++(-0.1,0);
\end{AnnotatedImage};
\end{frame}
\end{document}
\includegraphics[page=..., crop=...]{<your pdf file>}to select page and fragment inside atikznode and add marks as is explained in Drawing on an image in TikZ – Ignasi Apr 27 '19 at 12:28