diffrent results by using diffrent homopolymer and microsates files(just diff in microsates size)

[ZooJooFoo]

Hi

I am running Msisensor V0.6 for some WES data.

Firstly，scanning the reference file by scan model，using different size of microsates by changing parameter -s msisensor scan -l 10 -m 50 -s 2 -r 5 -d ref.fa -o microsatellites.2.list msisensor scan -l 10 -m 50 -s 1 -r 5 -d ref.fa -o microsatellites.1.list Note：microsatellites.1.list is completely contained in microsatellites.2.list

Sencondly，calling msi by files builded by step1： msisensor msi -c 20 -l 10 -p 10 -m 50 -q 5 -s 5 -w 40 -d microsatellites.2.list -n normal.bam -t tumor.bam -e panel.bed -o out.2 msisensor msi -c 20 -l 10 -p 10 -m 50 -q 5 -s 5 -w 40 -d microsatellites.1.list -n normal.bam -t tumor.bam -e panel.bed -o out.1

But i got a unexpected result，out.1 has more msi sites than out.2 out.1：2100 13 0.62 out.2：4709 6 0.13

Then i checked the _somatic and _dis files of some msi loci only exist in out.1，the dis files are totally same，but just not called by microsatellites.2.list file，it is confusing

I guess there maybe some different algorithm in calling msi by using different microsate size? Is there an explanation for this?

Thank you very much for all your help and developing MSISensor. Appreciate it

Sen

[PengJia6]

@ZooJooFoo Are the microsatellite loci in microsatellites.2.list and microsatellites.1.list the same? The difference between them may lead to different results later.