calling variants between two strains

Question

[steven.lin.pur]

(newbie alert)

I'm trying to find the sites of variants between two strains. I've map them both to the same reference. However, I don't know what the next step should be. I've used freebayes to call the SNP between the strains and the reference, but I don't know how to find the variants between the two strains themselves. Should I manipulate the 2 vcf files produced by calling SNP between the strains and reference, or is there a tool that I can use to call variants between the 2 strains themselves?

Thanks a lot!

Answer 1

[apelin20]

You need to merge (vcf-merge) the two VCF files you have. Take a look at vcf-compare also. It will tell you how many differences to reference your two strains have and how many differences are unique to each strain.

[steven.lin.pur]

Thank you for the advice. I have some problems when practicing it however, can you please help me?

When I merge and compare the two VCF files, I can't tell if there is a difference between the two strains when the following case occur:

Reference has a genotype A at locus 100;

Strain i has a genotype C at locus 100;

Strain j does not have a variant found at locus 100;

in such a case I can't tell if strain j is different from strain i at locus 100 or not. Because the lack of variant in strain j might be due to either lack of data(in which case it might actually be the same as strain i) or lack of variation from the reference(in which case its genotype is A and is a SNP against strain i).

I'm planning on using the SNPs to perform QTL mapping. I thought that genome wide SNP calling for QTL mapping is a common method used and that there should be a tool that calls the SNP between two strains directly, but I've looked up Gatk, samtools, freebayes and I can't seem to find any of it doing this...

Answer 2

[poisonAlien]

Why not use Mummer to align two strains directly?

[steven.lin.pur]

Thank you for the great advice!

it is my understanding that Mummer needs a reference too to perform alignment.

are you suggesting that I map one of the strain to the reference, creating a aligned genome of one strain, then used that aligned genome as a reference to map the other strain? Thanks again

[poisonAlien]

Hi, Mummer is better option if you have reference genome for both strains. We have used it in past to align two starins of yeast (S288C and YJM789) to determine genome wide difference. In your case if you dont have reference genomes for both strains, then you can do as suggested in above answer (vcf compare).

Or if you dont mind trying out different options, assemble genomes for both strains using velvet and use them to compare using Mummer.