Re: [Samtools-help] new user

[Tom B. <tb...@um...>]

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 <cb...@gc...>
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
>
>
>
>
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