I've designed 27 MSI probes to capture the reads.
As suggested, I used msisensor to obtain whether the loci was stable or not.
I restricted the msi site to those 27 MSI sites I designed, and used the default parameter for msi detection.
/bioinfo/software/msisensor2/msisensor2 msi -M /bioinfo/software/msisensor2/models_hg19/ -d ctdnawise-data/27_marker_microsatellites.list -t intermediate_bam/IDCL1017-GW9T0064D08_L3.markdup.bam -o example2.tumor.output
The output showed that only 7 have enough coverage
Since the reads distribution of these 27 sites seem quite normal, it made me quite confused.
Can anyone give me some suggestions to deal with such case?