Re: [FORGED] SNAPP SNP analysis with RAD-seq missing data

[Remco Bouckaert]

Hi Erika,

SNAPP interprets the numbers in the sequences as number of ‘red’ lineages, assuming the remainder are ‘green’. Since you mention there are 0s, 1s and 2s, I assume you have diploid data. If so, a zero is not interpreted as missing data, but as a site where there are no ‘red’s and 2 ‘green’s. Likewise, a 1 is interpreted as 1 ‘red’ and 1 ‘green’ and a 2 as no ‘red’ and 2 ‘green’s.

Cheers,

Remco

On 18/02/2016, at 1:04 pm, Erika <polupo...@gmail.com> wrote:

I am trying to analyze SNP data using SNAPP in BEAST 2.3.2 and am not quite sure that I am setting up the xml file correctly. This is what I have done:

1) Extracted unlinked, biallelic SNPs from my 15 RAD-seq libraries

2) Converted the vcf file into a binary nexus file using PGDSpider. This produced a file with 0s,1s, and 2s. I am assuming the 0s are missing data at a specific locus for a specific library.

3) Imported binary nexus file into BEAUti. Checked the box indicating that I have non-polymorphic sites, which are represented by the 0s (the missing data), calculated u and v from the data, and kept all other default parameters.

4) In the xml file generated by BEAUti the "total count", next to "sequence id" and "taxon" for each individual, was set to "4" by BEAUti but when I tried to get it to run in BEAST it said I needed to change "total count" to 3 for diploid individuals. I did this and it worked and the file is able to run in BEAST with no errors.

I just wanted to make sure that I have set up the xml file correctly and that I am supposed to select "non-polymorphic" sites when I have missing data coded as 0s.

Does this look correct?

 

BEAST output:

Rate prior = gamma

Log Likelihood Correction = -11512.481521921498

15 taxa

12685 sites with weight 13629

4065 patterns

Thank you

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.
Visit this group at https://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.