SNP calling from multiple genotypes

[sgcsd]

Hi
I am new to snp discovery analysis. We recently sequenced a wild type and two mutant lines using illumine. The wild type is different from the reference genome available. Can anyone suggest a pipeline for identifying the SNPs in WT-Mutant.

Do we need to assemble our WT before calling SNPs in mutant or can we use the reference genome to map the reads from both the WT and mutant and call the SNPs.

Appreciate your help.
Thank you

[vivek_]

I think you'd go through the SNP calling in the same way for both sets of samples. (i.e.., mapping to reference genome and calling SNPs using GATK/Samtools etc).

Then you could look at the common SNPs in dbSNP for the wild type strain and flag them in your wildtype variant files as being down to strain difference and proceed with the analysis for the remaining variants.

[sgcsd]

Thank you vivek.
So what I understood is run the SNP pipeline for both WT and mutant the same way and after we get the SNP file filter the common ones and focus on the SNPs different in both.

[vivek_]

Thank you vivek.
So what I understood is run the SNP pipeline for both WT and mutant the same way and after we get the SNP file filter the common ones and focus on the SNPs different in both.

yes, you'd just have to download the strain specific mutations VCF from dbSNP to find the mutations that are common to your wild-type strain because of the strain differences between wildtype and mouse reference genome.

[sgcsd]

thank you vivek