New to SNP analysis

[susanklein]

Hi,

I'm quite new to SNP analysis and I there's something I think should be simple to do but I cannot find any existing programs to help me. I want to find all the SNPs that are candidates for differences between two bacterial strains. I've tried programs like Harvest Suite, which is nice for viewing the SNPs but it can't output what I need: i.e. a list of SNPs that are fixed and different between the groups (akin to private alleles in a classical mapping). I could view them all manually, but that seems silly when it should be a simple thing to automatically output.

I'm hoping I don't have to write a script to parse the VCF files.. I hate those files..

Thanks for any help,

Susan

[HESmith]

GATK (Select Variants) or BedTools (subtract) can be used to filter multiple VCF files for common or unique SNPs.

[GenoMax]

vcftools/bcftools are additional options to manipulate VCF files.

[susanklein]

SNP interactions

Hi,

ok, thanks yes I saw those but they didn't quite do what I wanted, So I wrote my own python script, but then I was told from the person who gave me the that they have continuous variable data for samples, not categories as I thought, hence I now need to actually correlate presence / absence of SNPs against multiple phenotype measurements.

But again, I have come up blank on existing programs.. is there anything that can do this? I guess that when a SNP has multiple states then a correlation has to be done for each separately so its not just as simple as one correlation per line of the .vcf.

Also what about interactions between snps? I have 127,000 in my dataset.. that's a lot of interactions to test!

Thanks for any advice,

S.

[susanklein]

I have just found something called GCTA that I think will do what I need.

http://www.complextraitgenomics.com/software/gcta/download.html

[wetSEQer]

When you generate the mpileup file, try use varscan2, it is very handy.