msisensor
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ding-lab
microsatellite instability detection using tumor only or paired tumor-normal data
this issue is to request ignoring dup reads as an option. gatk best practice is to keep all duplicates in the bam, and i have read from a few issues...
Hello, Thank you for the msisensor tool. I have 2 questions: 1. I am using bam files after the GATK workflow. Is this a valid input for msisensor? 2. I...
What's the difference between output.prefix_germline file and output.prefix_somatic file, and why some of their MSI loci are same.How did you get the MSI loci in the output.prefix_germline file?
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...
Hi, I could find the locations of all the somatic sites in the file output.prefix_somatic. Could I get the locations of total sites analyzed somewhere? They should be a part...
README was set to _dis_tab in May 2018 [[commit](https://github.com/ding-lab/msisensor/commit/290271a1e6d369d701f4dcbf08f87569aeea7369), then the sample.cpp was changed to output _dis in June 2018 [[commit](https://github.com/ding-lab/msisensor/commit/38bc6549cd8ca119e562116897da6e529b3ed940)].
When I ran Msisensor， I found the results are quite different between using the deduplicated bam and not deduplicated bam. I wonder which bam shoud be used , the deduplicated...
Hi, Thank you for your improvment for tumor-only analysis. Could you give us more informations about the method used please ? Bests, Elodie
Hello, I have got the output files for tumor only BAMs. I would like to run Plot.R script. But I dont know which file I should use as input to...
Hi, I'm wondering how to assess the 5-marker/ 7-marker positivity from the output of msisensor, as the result indicated in the supplementary table of the paper? Also, could you tell...
