Chris -
There must be oodles of journal articles over the years since about 2010 in
the biology literatrure describing this analysis for non-human species. I
have no experience myself with non-human species. A very vanilla workflow
using bwa-mem and samtools is briefly described at
https://www.htslib.org/workflow/wgs-call.html. The Broad Institute GATK
suite of tools has very extensive and detailed documentation.
https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-
is one example. But as an introduction, the right journal article will
probably be more useful than either of these technical web pages.
- thanks - tom blackwell -
On Tue, Oct 24, 2023 at 6:10 AM Christopher Blair <cbl...@gc.cuny.edu>
wrote:
> Hi all,
>
> I was hoping that someone could point me in the right direction for
> processing WGS data for phylogenetics and population genetics. I will soon
> have 10x whole genome data for about 27 individuals of a lizard species. I
> will need to go from raw reads to multiple sequence alignments and
> SNPs/genotypes. There is a reference genome available from a closely
> related species. Any guidance would be appreciated.
>
>
> Chris
>
>
>
>
> <{===================~~~~~~~~~~~
> /\ /\
> Christopher Blair, Ph.D.
> Executive Officer, Biology PhD Program
>
> Professor
>
> Graduate Center and
>
> New York City College of Technology
> The City University of New York
> cbl...@citytech.cuny.edu <cbl...@gc.cuny.edu>; cbl...@gc.cuny.edu
> Website: https://sites.google.com/site/christopherblairphd/home
> Office: 4315 (GC); Academic Complex 501D (City Tech)
> Lab: Academic Complex 401 (City Tech)
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
