Question: How To Call Snp From .Ab1 Files Of Sanger Sequencing?
3
gravatar for michealsmith
6.8 years ago by
michealsmith740
michealsmith740 wrote:

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!

snp • 6.8k views
ADD COMMENTlink modified 16 months ago by jawhar.saks10 • written 6.8 years ago by michealsmith740

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

ADD REPLYlink written 16 months ago by jawhar.saks10
4
gravatar for Yahan
6.8 years ago by
Yahan370
Belgium
Yahan370 wrote:

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.

ADD COMMENTlink written 6.8 years ago by Yahan370
1

Many thanks! THis works like magic!

ADD REPLYlink written 6.8 years ago by michealsmith740

how about indel calling?

ADD REPLYlink written 3.4 years ago by liangzebin556630

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

ADD REPLYlink written 3.3 years ago by Amirosein70

For InDel discovery we recently set up Indigo http://gear.embl.de/indigo that can also decompose a het. indel in a Sanger Chromatogram.

ADD REPLYlink written 2.7 years ago by trausch1.4k
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