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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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feature request: indicate deletion or insertions #35

Closed kcleal closed 2 years ago

kcleal commented 2 years ago

In tumor/normal mode, how can I tell if a site is a deletion or insertion in the tumor? I can only see a difference column. It might be more useful to report something like tumor content / normal content rather than (AreaMax - AreaMin)/AreaMax

PengJia6 commented 2 years ago

@kcleal do you mean tumor purity？

kcleal commented 2 years ago

Sorry, I mean for the sites that are identified in the somatic output file .e.g:

chromosome  location    left_flank_bases    repeat_times    repeat_unit_bases   right_flank_bases   difference  P_value FDR rank

chr3    54867528    GCTTT   14  A   GGCCT   0.92857 1.028e-06   0.027473    1

When I look at this loci in IGV, I can see that the 'tumor' sample is homozygous for a 4bp deletion, whereas the 'normal' sample is heterozygous with a 3bp and a 4bp deletion. So the tumor has an extra 'deletion' (normal top pane, tumor bottom pane):

Screenshot 2021-09-06 at 10 47 04

An example of an 'insertion' site is

chr13   64153219    TTTTC   13  T   GAAAA   0.84211 8.6836e-06  0.021096    11
Screenshot 2021-09-06 at 10 54 19

Here the 'tumor' sample has an extra 1bp added to one of the alleles.

From the output, im not sure it is possible to distinguish deletion sites from insertion sites in the tumor. Hope that makes sense

PengJia6 commented 2 years ago

Thanks for your clarification, MSIsensor-pro (msi command) just compare the tumor and normal sequence read in microsatellite regions and tell you if it is a somatic mutation or not and final we report the msi score. We do not report a details like deletion or insertion of microsatellite. I think you may try somatic mutation caller like mutect2.