How to determine specific strains(mouse) from BAM(or VCF) by unknown sample? (using or not using dbSNPs)
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4 months ago
askif4 ▴ 10

I have downloaded the mouse strain-specific VCF files(dbSNP) from Sanger institute.

And I have my own VCF files of C57, Balb/C mouse.

I want to compare my vcf files with Sanger VCF files in order to find

which dbSNPs will match the most with my VCF files.

I used 'vcf-compare' from vcftoolz.

But the results were not what I expected.

The result showed positions, SNPs with venn diagram.

But there were no shared SNPs even with same strains.

I don't know what is the problem with this...

If you could help me with this issues or could recommend some tools to

infer strains with VCF files(or BAM), It would be greatful

Thank you.

SNP VCF dbSNP mouse • 213 views
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