once again thank you for providing this tool and the great effort you put into this project.
I am currently struggling to set up PureCN correctly and/or to interpret the results. I have WES data of tumor patients without matched normal. The tumor material is FFPE derived and for quite a lot of these samples I also see quite a lot of noise. Some parameters of my workflow:
variant calling is done with Mutect2, I use a padded target interval file (50bp), the flags --genotype-germline-sites true --genotype-pon-sites true are used, I use a PoN with 30 samples
PureCN is then run with the internal segmentation, a bait bed file could not be provided by the manufacturer, so I had to use the target bed file, the NormalDB was created with the PoN generated with Mutect2, there were too few off target counts so I had to remove the --off-target flag and re-run.
For all of my samples I get a poor goodness of fit flag. A log file of representative samples is attached and here is a snippet:
Do you have an idea what might cause this issue? Thank you so much for your help!
Dear Marcus,
once again thank you for providing this tool and the great effort you put into this project.
I am currently struggling to set up PureCN correctly and/or to interpret the results. I have WES data of tumor patients without matched normal. The tumor material is FFPE derived and for quite a lot of these samples I also see quite a lot of noise. Some parameters of my workflow:
For all of my samples I get a poor goodness of fit flag. A log file of representative samples is attached and here is a snippet:![image](https://github.com/lima1/PureCN/assets/235535/ad430a9d-0ff2-47e2-a7c7-2f548cc8e800)
Do you have an idea what might cause this issue? Thank you so much for your help!
Best, Moritz S81_copy.log