Distance matrix from coloured graph

[Carlos Talavera Lopez]

Hi

I have been playing around with the idea of creating a targeted phylogenetic analysis by creating a distance matrix out of the CORTEX_VAR graph. 

I have notice that the question has been posted before; nevertheless I would like to ask if you could provide some more details or even strategies 

to do it properly. 

Thanks in advance

[Zamin Iqbal]

Hi Carlos,

You asked me about this before and I forgot to reply, sorry.

So, the purest way to do it is

1. Use --ref Absent in run_calls.pl (no reference), and then make a distance matrix from SNP calls with reasonable genotypes (eg max (GT_CONF) must be >2 say)

More normally you can use any standard method from the Cortex VCF.

Another option is 

a) dump supernodes (=unitigs) --output_supernodes, and then use that as input for --pan_genome_matrix, giving a similarity matrix

Z