Question: VariantCalling with single sanger read
0
gravatar for Amirosein
3.3 years ago by
Amirosein70
UBC, Vancouver, CA.
Amirosein70 wrote:

Hi All

I want to do VariantCalling but with a single sanger read in a single specific region (so i can't use routine VariantCalling pipelines). for example i have a sanger read from a region of a gene and i know that gene, now i want to tell Genomic Poisition of Homozygous and Heterozygous events.

i used sangerseqR package for proccessing and working with sanger read, now i have a single sequence(primary sequence, not sanger anymore) and a reference(taht gene), is there any function or package which can compare them and return genomic positions of Homozygous events in that query sequence ?

thanks a lot

blast variantcalling snps indel • 1.1k views
ADD COMMENTlink modified 10 months ago by trausch1.4k • written 3.3 years ago by Amirosein70
1
gravatar for Dan Gaston
3.3 years ago by
Dan Gaston7.1k
Canada
Dan Gaston7.1k wrote:

You probably want to use the MakeBaseCalls function of sangerseqR. That will give you heterozygous events, all other positions are homozygous.

ADD COMMENTlink written 3.3 years ago by Dan Gaston7.1k
1

Make sure to look at the actual traces at your variant position(s). When it comes to sanger seq, no algorithm i've come accross beats eyes on the trace for working out if the variant is real or not.

ADD REPLYlink written 3.3 years ago by i.sudbery6.3k
1

Absolutely second this.

ADD REPLYlink written 3.3 years ago by Dan Gaston7.1k
1
gravatar for Charles Warden
3.3 years ago by
Charles Warden7.5k
Duarte, CA
Charles Warden7.5k wrote:

You can use the Staden package, but there might be a bit of a learning curve with getting used to the interface:

http://staden.sourceforge.net/manual/mutations_unix_toc.html#SEC1

http://staden.sourceforge.net/

ADD COMMENTlink written 3.3 years ago by Charles Warden7.5k
1
gravatar for WouterDeCoster
3.3 years ago by
Belgium
WouterDeCoster42k wrote:

Developed in my department and great piece of software: http://www.molgen.ua.ac.be/bioinfo/novosnp/

(I wasn't involved in the development, I'm just a user.)

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by WouterDeCoster42k
0
gravatar for jawhar.saks
10 months ago by
jawhar.saks10
France
jawhar.saks10 wrote:

Hello,

We developed an automatic software working on batches and allowing for optionnal conclusion files based on theorical mutation position following papers rules.

IAGE Tools Analytics : A solution to detect SNP and INDELS from Sanger in CRISPR analysis workflow.

Video of the software.

Is that what you are looking for ?

ADD COMMENTlink written 10 months ago by jawhar.saks10

By the way, our software outputs for each sanger file (.ab1) a folder with in it :

  • Plus.fasta
  • Minus.fasta
  • Plus_Wt.aln
  • Minus_WT.aln
  • Chromatogram

And the conclusion files for the batch if a theorical position of mutation is given.

ADD REPLYlink written 10 months ago by jawhar.saks10
0
gravatar for trausch
10 months ago by
trausch1.4k
Germany
trausch1.4k wrote:

Indigo outputs a BCF file with variant calls for Sanger sequencing: https://www.gear-genomics.com/indigo/

ADD COMMENTlink modified 11 weeks ago • written 10 months ago by trausch1.4k
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