VariantCalling with single sanger read

Question

[Amirosein]

Hi All

I want to do Variant Calling 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 Position of Homozygous and Heterozygous events.

I used sangerseqR package for processing and working with sanger read, now I have a single sequence(primary sequence, not sanger anymore) and a reference (that 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

Answer 1

[DG]

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

[i.sudbery]

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.

[DG]

Absolutely second this.

Answer 2

[Charles Warden]

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/

Answer 3

[WouterDeCoster]

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.)

Answer 4

[jawhar.saks]

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 ?

[jawhar.saks]

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.

Answer 5

[trausch]

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