FAANG List Archived Post

From hendrik-jan.megens@wur.nl  Mon May 18 08:15:48 2015
From: "Megens, Hendrik-Jan" <hendrik-jan.megens@wur.nl>
Subject: RE: Bioinformatics pipelines to analyze FAANG data
Date: Mon, 18 May 2015 13:08:44 +0000
To: Multiple Recipients of <faang@animalgenome.org>

Hi Mick, Laura,

including population level data will be important. Resources, both sequencing
and (HD) genotyping are out there in several labs and when integrated would
make a huge contribution towards better genotype calls and subsequent
annotation. Annotations ideally be kept close to Ensembl resources (VEP, EVA,
etc).

Very much interested in this myself, so count me in for this working group
please.

Cheers,
Hendrik-Jan

----------------------
- H-J Megens, PhD,
- Assistant Professor / Head of Bioinformatics,
- Animal Breeding & Genomics Centre,
- Wageningen University,
- Wageningen, The Netherlands
- LinkedIn: http://nl.linkedin.com/pub/hendrik-jan-megens/24/536/2b8
- Google Scholar: http://scholar.google.nl/citations?user=3DkGUIXOYAAAAJ

________________________________________
.From: WATSON Mick [mick.watsonroslin.ed.ac.uk].Sent: Monday, May 18, 2015 9:42
AM
.To: Multiple Recipients of
.Subject: RE: Bioinformatics pipelines to analyze FAANG data

Hi Martien

Excellent, I am glad to see we are not alone!

For the validated SNP sets we use to train models, the SNP chip variants are
a great place to start - but from there it seems to make sense to me to double
check and make sure: i) variants are not in poor quality areas of the genome;
ii) variants are in, or close to, hardy-weinberg equilibrium in at least one
study.  Perhaps much of this has already been done in the array design, but
it would be unusual for there to be no false positive SNPs on each array, and
we should attempt to filter these out :-)

Indels are an interesting one - very high false positive rate in all studies
I know about.

Laura, do you know anything about how the GATK human indel reference sets were
created?  1000G_phase1.indels.b37.vcf and
Mills_and_1000G_gold_standard.indels.b37.sites.vcf?

Cheers
Mick