How To Call Snp From .Ab1 Files Of Sanger Sequencing?

Question

[michealsmith]

I've got a bunch of .ab1 files from sanger sequencing over an exon. Any free programs to quickly find the SNP?

I tried to convert .ab1 to fastq (use Staden package) with the intention to use BWA; but it turns out Staden is an assembly program which gives me one long config from which I cannot call SNP. I guess there could be some commands from Staden that can do the job, but it has a monsterous manual with 700 pages...

So any quick way to call SNP from .ab1 file?

Thanks!

[jawhar.saks]

I've got a solution for this problem, mp me if you want.

Answer 1

[Yahan]

Check out novoSnp

http://www.molgen.ua.ac.be/bioinfo/novosnp/

This program will align your ab1 files on a reference in fasta format and call snps, which you can then validate.

Free for academic use.

There's a linux and windows version.

[michealsmith]

Many thanks! THis works like magic!

[liangzebin5566]

how about indel calling?

[Amirosein]

only for SNP calling? is it able to find all point mutations or/and indels?

[trausch]

Indigo (http://www.gear-genomics.com/indigo) calls SNPs and InDels in Sanger Chromatogram files.