Best Protocol to view SNPs

[shoncho]

Dear Next-gen fans,
I am attempting to identify and view SNPs from my single end Solexa data. I have done alignment in Bowtie and have been attempting to identify SNPs and Indels using SAMTools but I cannot find a viewer that will let me visualize them in context.
1. Is there a better program available to find SNPs?
2. Is there a preferred viewer to use to visualize said SNPS?


- Cheers,

S Honco

[GW_OK]

Have you tried the UCSC Genome Browser? I usually upload my SNP calls as custom tracks.

[shoncho]

I have tried Genome Browser, both the one found at UCSC and my institute's local version, but only for my alignments. What format do you use to upload them as custom tracks?

[GW_OK]

.bed format:

Chromosome_StartCoord_StopCoord_YourSNPName

chr6 32145398 32145399 (G/C)

[genbio64]

Yes that would work. Is there a script available to do that otherwise I will be parsing many SNPs by hand?

[GW_OK]

CLC (what I'm using) exports SNP calls as csv files containing SNP coordinate and variant. I just import to Excel, insert a column of cells with chromosome number, insert another column of cells for the start coordinate as (CLC coordinate)-1, and then copy/paste the four columns into a text editor.

[genbio64]

Sure, CLC is a great piece of software, if you have it. My lab does not so I am forced to stick with the open source route.

[GW_OK]

Well, what type of file is your SNP caller spitting out?

[Dongliang Ge]

Folks,

You may also want to check this out:

http://www.svaproject.org/

We develop SequenceVariantAnalyzer, or SVA, trying to annotate and visualize SNP, INDEL, and larger SVs.

[Dongliang Ge]

Another screenshot:



You can find larger screenshots here:

http://www.svaproject.org/screenshot1.php

[genbio64]

So far the SNP output I can produce comes out of Bowtie, so pileup or a generic text format.

[GW_OK]

If you can get it in tab delimited format you can import to Excel like I mentioned before.

[genbio64]

@Donglian Ge
Your URL is broken.

[Dongliang Ge]

@Donglian Ge
Your URL is broken.

Try this out:

Homepage:

http://people.genome.duke.edu/~dg48/sva/

Screenshots:

http://people.genome.duke.edu/~dg48/sva/screenshots.php

Maybe due to DNS server? I just set the new domain this week. It works here.

What internet browser are you using? - Maybe I can test the new domain with that browser?

Thanks. Let me know.

[lh3]

If it were me, I would convert the SNP output to BED and load them into IGV along with the alignment and annotations. There is a thread on RNA-seq visualization and most of discussions there are applied here.