Output docs + pN/pS ratio

[PegahDan]

Hi @metaGmetapop ! I used your tool on my data (it ran perfectly!) and I have a few questions.

1. Is there a link to where find detailed explanations of the output files we get and maybe their columns ? For example, a_ct, g_ct, ... columns.
2. This question is related to the first one and might seem naive. How is the pN/pS ratio computed exactly ?
3. How can we use your tool to bypass the pre-process and other first steps, to directly compute macro and micro indices directly by giving VCF files ?

Tanks a lot !

[gregoryannc]

I'm glad you got it running and it worked for you! Sorry for the late reply. There was a bit of an issue with the update with the samtools conda version!

1. For the columns, the a_ct is the number of A variants at the loci, etc.
2. The pN/pS ratio is calculated using the method described in Schloissnig et al. 2013 Nature (https://www.nature.com/articles/nature11711)
3. As of now, we do not have bypass method because we want to ensure that the filtering of the datasets was universally applied.

Please let us know if you have any other questions!