Question: Variant calling for sanger reads
2
gravatar for Amirosein
2.7 years ago by
Amirosein70
UBC, Vancouver, CA.
Amirosein70 wrote:

Hello all i have a Sanger read (an *.ab1 file which i did basecalling for it) and a reference. i want to find homo and hetero events for this sample (read) for further computations like annotating individual variants. now i did it myself but it seems there is a standard pipeline for this purpose for NGS reads. is there any pipeline for sanger reads as well? or i need to convert my read into fastq for this purpose? and what if "yes" what is the pipeline? i'm using Rstudio Bioconductor.

thanks all

ADD COMMENTlink modified 2.7 years ago by Keith Callenberg890 • written 2.7 years ago by Amirosein70
0
gravatar for i.sudbery
2.7 years ago by
i.sudbery4.4k
Sheffield, UK
i.sudbery4.4k wrote:

Back in the day we used to use GAP4. Its not quite what you'd call "automated", but it makes a start. With sanger sequencing, because of the low coverage, you need to examine the sequence traces at any suspected SNPs yourself, or at least you did last time I did it.

Another free tool to do this was ExoTrace.

I don't know if either of these are still available.

I've also used software called MutationSurveyor, which is apparently still available, but isn't free.

ADD COMMENTlink written 2.7 years ago by i.sudbery4.4k
0
gravatar for Keith Callenberg
2.7 years ago by
Pittsburgh, PA
Keith Callenberg890 wrote:

It does not look to me like variant calling from .ab1 files has been implemented in any publicly-available R/Bioconductor packages. The one sanger popular sanger package will perform basecalling and alignment, but stops short of variant calling: https://www.bioconductor.org/packages/devel/bioc/vignettes/sangerseqR/inst/doc/sangerseq_walkthrough.pdf

If you can step away from R, AutoCSA looks like it would meet your needs. It reads from .ab1 files directly, is free, java-based, and it looks like it can be automated to be included in a pipeline.

Also, novoSNP is a GUI-based desktop application that might be a useful reference.

There are some useful references also in this thread: Is there a way to access the data stored in a .ab1 file ?

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Keith Callenberg890
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 524 users visited in the last hour