filtering on merged samples

[cheesemania]

Great tool!

I have a quick question on filtering by kmer coverage is samples which are run as batches. How would the "bayestyper_genomic_parameters.txt" file be specified after runs have been combined (or does filtering need to be done prior to combining samples?)

Thanks

[jonassibbesen]

Thanks, glad you like the tool.

Filtering is automatically done by the genotyping module (bayesTyper genotype) on each batch. If you are interested in re-filtering on the combined set you can concatenate all the "bayestyper_genomic_parameters.txt" files into a single file and use that as input.

Note that the genotype posterior and the kmer filtering will be unchanged (if the same parameters are used) on the combined set, since they are all applied on the sample level. This is, however, not the case for the "min-homozygote-genotypes" filter, which is calculated across all samples and thus will be different on the combined set.

Hope it helps. Let me know if you have any other question.

Cheers,

Jonas