Comments (7)
liangkaiye
commented on September 3, 2024
What is your sequence coverage?
Hi,
Thank you for providing a comprehensive tool. I am currently running MSIsensor on WGS and WES done on the same sample.
While I do get some % value for the Exome, for the WGS it only detects 1 somatic site. I am running the command exactly like provided in the README.
Any help with understanding what is going on is much appreciated.
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Rashesh7
commented on September 3, 2024
Normal= 40X and Tumor=80X
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liangkaiye
commented on September 3, 2024
What is the MSI score? If not a MSI-H sample, we do not expect many somatic sites.
Normal= 40X and Tumor=80X
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Rashesh7
commented on September 3, 2024
The output for the Exome is:
Total_Number_of_Sites Number_of_Somatic_Sites %
1506 11 0.73
For the WGS is:
Total_Number_of_Sites Number_of_Somatic_Sites %
4474 1 0.02
I am using the example.bed file given in the test directory. So probably it is not an MSI-H sample. But it should still give me similar number of Somatic sites for WGS and WXS, right?
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liangkaiye
commented on September 3, 2024
This is a MSS sample based on percentage. The numbers of somatic sites differ because of the coverage issue. If a site has fewer than 20 reads in both tumor and normal, this site is not considered as candidate site at all.
Kai
The output for the Exome is:
Total_Number_of_Sites Number_of_Somatic_Sites %
1506 11 0.73
For the WGS is:
Total_Number_of_Sites Number_of_Somatic_Sites %
4474 1 0.02
I am using the example.bed file given in the test directory.
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Rashesh7
commented on September 3, 2024
But then that should affect the "Total_Number_of_Sites" and not just the "Number_of_Somatic_Sites".
Or do you mean that, the 11 somatic sites in Exome might not be covered > 20X in WGS. So even though the total number of sites increased, we lost the somatic once due to coverage
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liangkaiye
commented on September 3, 2024
The latter one is the reason.
But then that should affect the "Total_Number_of_Sites" and not just the "Number_of_Somatic_Sites".
Or do you mean that, the 11 somatic sites in Exome might not be covered > 20X in WGS. So even though the total number of sites increased, we lost the somatic once due to coverage
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Related Issues (20)
- whether to use deduplicated bam HOT 14
- error while loading shared libraries HOT 1
- How difference value is calculated HOT 1
- can't find the description of the result file : output.prefix: msi score output HOT 3
- minimal comentropy threshold HOT 1
- Error "Same reference genome file should be used in both 'msisensor scan' and 'msisensor msi' steps!!!" HOT 2
- How to prepare correct bed file for msisensor msi? HOT 2
- Microsatellite loci for hg38 HOT 3
- Tagging release 0.6 HOT 3
- failed to open output files to write HOT 2
- How msisensor deal with soft clipping reads? HOT 1
- Bed file not loading HOT 1
- msisensor on whole exome HOT 1
- Get location of total sites HOT 1
- Reference genome issues in msisensor and number of somatic sites prediction in msisensor2 HOT 3
- The MSI loci in output.prefix_germline file HOT 1
- msisensor2 requires write permission to the models directory HOT 1
- MSI score greater than 1
- bam files after realignment & output_dis file
- feature request: ignore duplicate-marked reads HOT 1
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