Reference genome issues in msisensor and number of somatic sites prediction in msisensor2

[Manonanthini]

Hi ,
I have a normal and tumor bam file from patient sample.I would like to view the micro satellites in the sample.I tried scanning reference genome hg38 and hg19 from ucsc genome browser.
I can create the micro satellites list file but with the file i am not able to proceed with finding scores and I am repeatedly getting the following error,
Same reference genome file should be used in both 'msisensor scan' and 'msisensor msi' steps!!!
I have questions like:

1. Is there any specific reference genome to use ?
2. I could run scan and msi score on the data with genome models in msisensor2 but i couldn't get any information on threshold value for MSI status. How much is the threshold for MSI status in msisensor2?
3. Also please explain the difference in number of somatic sites and msi score in matched tumor-normal and tumor only options. Which one I should use for reliable result?
   Please reply.

[Beifang]

Since you have paired tumor and normal bams, please figure out what kind of reference genomes used in these bams and then try msisensor. You can also do realignment for these bams using hg38 or hg19 ref in hand.

[Manonanthini]

I have tried hg38 aligned bam file with same reference genome hg38 as well as hg19 aligned bam file with hg19 reference genome using 'scan' module in msisensor.

[Manonanthini]

msierror.txt
Hi ,
Is there any specific reference genome i have to use? I used ucsc hg38 and hg19 but the program is getting aborted before ending .Please guide me to proceed.Herewith I have attached the commands and error I got .