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• take gstacks output as reference
• map individuals with bwa
• call variants with varlociraptor

Currently, for low contamination samples, plot_kmer_mapping output will be all black, because it takes the first 100 reads or so. Instead, we should take the first 100 classified reads.

The current report is too large. The reason is that we put uncompressed, unfiltered raw results there. It is though rather meant for end results that would also appear in a paper (plots and tables).

Hi @johanneskoester,

Is it possible to run this analyses starting from raw reads? Also, could you provide an example of the samples.tsv file?

Thank you,
Susheel

The populations script supports output in fasta, genepop, and other formats. To avoid writing unwanted files it would be helpful to specify the desired output types in the config file.

Hi,
The shell command in the rule "generate_consensus_reads" make a call to a command named rbt_release which is missing in the repo.

This is also missing in the dependencies section of envs/consensus.yaml

Regards

E.g.: calculate concordance between replicates, allow to use that in order to select a good parameter set. This might be obsoleted by #11. Hence it should not be considered before #11 is complete.

Plot a histogram of pairwise edit distances between loci (perhaps with Myers bitparallel algorithm).