Adding more filters than are in the Common_config

[albinap]

Can I somehow add the -minIndDepth filter (Only use site if at least minInd of samples has this minimum depth) to the Common_config file or other config files? I have found it to be very important to deal with missing data when comparing ancient and modern genomes.

I would also like to add these filters which I have also found to be important for my dataset
-setMinDepth
-setMaxDepth
-rmTrans
-minMaf
-SNP_pval 1e-6

[shamanpi]

Hi Albína,

We should have a fix in the next week or two for advanced argument use. Right now, however, there's no way to add optional arguments to the config files, so you would have to edit the wrapper files directly to use those flags. You'd also have to add a "-doCounts" flag to the wrappers while using the depth-based filters.

[albinap]

Ok excellent, I will await the fix since it is so imminent