-f option

[lys1001s]

Hi, thank you for making this tool!

I used this code below without -M option for tumor-only sample: {msisensor2} msi -d {microsatellites_list} -f 0.5 -t {input.tumor} -o {output}

The result is just the same as when -f options was at default(0.05).

Could you figure out why?

Thank you

[Beifang]

-f option doesn't have any effect on msisensor2.

[lys1001s]

Then is there any option or method to change the FDR threshold? I need it for tumor only case.

[Beifang]

you can adjust msisensor score threshold for different sequecning depth data.

[Beifang]

since the impact of variant sequencing depths, we will release new version to solve that.

[lys1001s]

Hi, thanks for reply! Could you explain 'you can adjust msisensor score threshold for different sequecning depth data.' in more detail?