variant annotation for yeast (saccer)

[christophpale]

Hi,
We have done WG hiseq sequencing of yeast strains s. cerevisiae
and I wanted to ask if anyone knows a program that can annotate
the variants (i.e. whether they are nonsynonmous or synonymous)
thanks
C

[laura]

you could try ensembl variant effect predictor

http://fungi.ensembl.org/tools.html

[HESmith]

We've used Annovar for S. cerevisiae SNP annotation. Be aware that the SNP density in yeast is fairly high, so you'll find a lot of variants.

[Jane M]

I have used Annovar but it doesn't seem to take into account the strand. Not easy with double stranded data...
So now, I will try the VariantAnnotation package from R.

[HESmith]

I have used Annovar but it doesn't seem to take into account the strand. Not easy with double stranded data...
So now, I will try the VariantAnnotation package from R.

Annovar provides annotation for SNP calls generated by another package (e.g., Samtools), so it's unclear why you think strandedness affects its operation.

[Jane M]

Annovar provides annotation for SNP calls generated by another package (e.g., Samtools), so it's unclear why you think strandedness affects its operation.

For me, the problem is that I provided the information that I have, wich are from direct and reverse senses.

1	12854480	12854480	G	A (+)
1	86890081	86890081	G	A (-)
#should be:
1	12854480	12854480	G	A (+)
1	86890081	86890081	C	T

I didn't pay attention to this fact. I didn't understand why I had the warning message according to which my reference alleles were wrong. I finally understood that I had to "transform the reverse strand information into direct strand information": find the reverse complement and probably change the mutation positions for all the information in reverse sense.

Of course, I can use Annovar, but first I have to treat the data. It seems that the R package can handle the reverse information.

[gruberjd]

Christoph and HESmith-- can I ask, what DNA extraction technique do you favor for yeast? I have gotten good results with a very baroque, old school protocol, but I need to do several hundred libraries. I'd like to switch to the kit we used before NGS (the Qiagen PureGene kit) but have been told that the dsDNA content is very low. Any advice for simplifying/speeding up the extractions?
Thanks!

[HESmith]

We've sequenced only a few yeast strains, and the protocol we used may be even older school than yours (it's the same one I used in grad school, and I graduated during the first Clinton administration...). It is assuredly not one you'd want to use for 100s of samples. Sorry I can't help; please post if you find something that works well.

-Harold