search

ANGSD-wrapper / angsd-wrapper

Utilities for analyzing next generation sequencing data.
MIT License
14 stars 4 forks source link

Adding more filters than are in the Common_config #6

Open albinap opened 4 years ago

albinap commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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